]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added load.logfile command. changed summary.single output for subsample=t.
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index f904a8b33650f30c1432f5866481b22a749ee2a9..6db66c6184bc3798ee4d8ba2fc7247a9feb6acb4 100644 (file)
@@ -3,44 +3,28 @@
        archiveVersion = 1;
        classes = {
        };
-       objectVersion = 45;
+       objectVersion = 46;
        objects = {
 
 /* Begin PBXBuildFile section */
+               219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */; };
+               219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */; };
                7E6BE10A12F710D8007ADDBE /* refchimeratest.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */; };
                8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */ = {isa = PBXBuildFile; fileRef = C6A0FF2C0290799A04C91782 /* mothur.1 */; };
+               A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056E5156A93D000924A2D /* getotulabelscommand.cpp */; };
+               A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */; };
                A70332B712D3A13400761E33 /* makefile in Sources */ = {isa = PBXBuildFile; fileRef = A70332B512D3A13400761E33 /* makefile */; };
                A713EBAC12DC7613000092AC /* readphylipvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBAB12DC7613000092AC /* readphylipvector.cpp */; };
                A713EBED12DC7C5E000092AC /* nmdscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */; };
                A71CB160130B04A2001E7287 /* anosimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71CB15E130B04A2001E7287 /* anosimcommand.cpp */; };
                A71FE12C12EDF72400963CA7 /* mergegroupscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */; };
                A721765713BB9F7D0014DAAE /* referencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A721765613BB9F7D0014DAAE /* referencedb.cpp */; };
+               A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A724D2B6153C8628000A826F /* makebiomcommand.cpp */; };
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+               A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */; };
                A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */; };
                A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */; };
                A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74A9A9E148E881E00AB5E3E /* spline.cpp */; };
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-               A74D3689137DAB8400332B0C /* alignchimel.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3657137DAB8300332B0C /* alignchimel.cpp */; };
-               A74D368A137DAB8400332B0C /* alnparams.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D365A137DAB8300332B0C /* alnparams.cpp */; };
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-               A74D368C137DAB8400332B0C /* alpha2.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D365E137DAB8300332B0C /* alpha2.cpp */; };
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-               A74D3694137DAB8400332B0C /* searchchime.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3674137DAB8300332B0C /* searchchime.cpp */; };
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-               A74D3696137DAB8400332B0C /* setnucmx.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3678137DAB8300332B0C /* setnucmx.cpp */; };
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-               A74D3698137DAB8400332B0C /* tracebackbit.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D367F137DAB8300332B0C /* tracebackbit.cpp */; };
-               A74D3699137DAB8400332B0C /* uchime_main.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3681137DAB8300332B0C /* uchime_main.cpp */; };
-               A74D369A137DAB8400332B0C /* usort.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3683137DAB8300332B0C /* usort.cpp */; };
-               A74D369B137DAB8400332B0C /* viterbifast.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A74D3684137DAB8300332B0C /* viterbifast.cpp */; };
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+               A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7876A25152A017C00A0AE86 /* subsample.cpp */; };
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+               A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */; };
+               A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */; };
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@@ -62,6 +49,7 @@
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                A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */; };
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@@ -76,7 +64,6 @@
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 /* Begin PBXFileReference section */
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+               219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcoremicrobiomecommand.cpp; sourceTree = "<group>"; };
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                7E6BE10812F710D8007ADDBE /* refchimeratest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = refchimeratest.h; sourceTree = "<group>"; };
                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = refchimeratest.cpp; sourceTree = "<group>"; };
                7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdistignorens.h; sourceTree = "<group>"; };
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+               A70056E5156A93D000924A2D /* getotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getotulabelscommand.cpp; sourceTree = "<group>"; };
+               A70056E8156A93E300924A2D /* getotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getotulabelscommand.h; sourceTree = "<group>"; };
+               A70056E9156AB6D400924A2D /* removeotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotulabelscommand.h; sourceTree = "<group>"; };
+               A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotulabelscommand.cpp; sourceTree = "<group>"; };
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                A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
                A713EBAB12DC7613000092AC /* readphylipvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylipvector.cpp; sourceTree = "<group>"; };
                A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergegroupscommand.cpp; sourceTree = "<group>"; };
                A721765513BB9F7D0014DAAE /* referencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = referencedb.h; sourceTree = "<group>"; };
                A721765613BB9F7D0014DAAE /* referencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = referencedb.cpp; sourceTree = "<group>"; };
+               A724D2B4153C8600000A826F /* makebiomcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makebiomcommand.h; sourceTree = "<group>"; };
+               A724D2B6153C8628000A826F /* makebiomcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makebiomcommand.cpp; sourceTree = "<group>"; };
                A727864212E9E28C00F86ABA /* removerarecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removerarecommand.h; sourceTree = "<group>"; };
                A727864312E9E28C00F86ABA /* removerarecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removerarecommand.cpp; sourceTree = "<group>"; };
+               A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = loadlogfilecommand.h; sourceTree = "<group>"; };
+               A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = loadlogfilecommand.cpp; sourceTree = "<group>"; };
                A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearmemorycommand.h; sourceTree = "<group>"; };
                A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearmemorycommand.cpp; sourceTree = "<group>"; };
                A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurmetastats.h; sourceTree = "<group>"; };
                A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurmetastats.cpp; sourceTree = "<group>"; };
                A74A9A9D148E881E00AB5E3E /* spline.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spline.h; sourceTree = "<group>"; };
                A74A9A9E148E881E00AB5E3E /* spline.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = spline.cpp; sourceTree = "<group>"; };
-               A74D3655137DAB8300332B0C /* addtargets2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = addtargets2.cpp; sourceTree = "<group>"; };
-               A74D3656137DAB8300332B0C /* alignchime.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignchime.cpp; sourceTree = "<group>"; };
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-               A74D365C137DAB8300332B0C /* alpha.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alpha.cpp; sourceTree = "<group>"; };
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-               A74D365E137DAB8300332B0C /* alpha2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alpha2.cpp; sourceTree = "<group>"; };
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                A79234D513C74BF6002B08E2 /* mothurfisher.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurfisher.h; sourceTree = "<group>"; };
                A79234D613C74BF6002B08E2 /* mothurfisher.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurfisher.cpp; sourceTree = "<group>"; };
                A795840B13F13CD900F201D5 /* countgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = countgroupscommand.h; sourceTree = "<group>"; };
                A795840C13F13CD900F201D5 /* countgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = countgroupscommand.cpp; sourceTree = "<group>"; };
                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makefastqcommand.h; sourceTree = "<group>"; };
                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makefastqcommand.cpp; sourceTree = "<group>"; };
+               A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listotulabelscommand.cpp; sourceTree = "<group>"; };
+               A7A0671C156294810095C8C5 /* listotulabelscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listotulabelscommand.h; sourceTree = "<group>"; };
+               A7A0671D1562AC230095C8C5 /* makecontigscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makecontigscommand.h; sourceTree = "<group>"; };
+               A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makecontigscommand.cpp; sourceTree = "<group>"; };
                A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sortseqscommand.cpp; sourceTree = "<group>"; };
                A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sortseqscommand.h; sourceTree = "<group>"; };
                A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuassociationcommand.cpp; sourceTree = "<group>"; };
                A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cooccurrencecommand.h; sourceTree = "<group>"; };
                A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trialSwap2.cpp; sourceTree = "<group>"; };
                A7C3DC0E14FE469500FE1924 /* trialswap2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trialswap2.h; sourceTree = "<group>"; };
+               A7D755D71535F665009BF21A /* treereader.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treereader.h; sourceTree = "<group>"; };
+               A7D755D91535F679009BF21A /* treereader.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treereader.cpp; sourceTree = "<group>"; };
                A7DAAFA3133A254E003956EB /* commandparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = commandparameter.h; sourceTree = "<group>"; };
                A7E9B64F12D37EC300DA6239 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                A7E9B65012D37EC300DA6239 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                A7E9B66712D37EC400DA6239 /* boneh.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = boneh.h; sourceTree = "<group>"; };
                A7E9B66812D37EC400DA6239 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = "<group>"; };
                A7E9B66912D37EC400DA6239 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = "<group>"; };
-               A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrapsharedcommand.cpp; sourceTree = "<group>"; };
-               A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrapsharedcommand.h; sourceTree = "<group>"; };
                A7E9B66C12D37EC400DA6239 /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = "<group>"; };
                A7E9B66D12D37EC400DA6239 /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = "<group>"; };
                A7E9B66E12D37EC400DA6239 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = "<group>"; };
                A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = SOURCE_ROOT; };
                A7E9B6B312D37EC400DA6239 /* common.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = common.h; sourceTree = "<group>"; };
                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; };
-               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = "<group>"; };
-               A7E9B6B612D37EC400DA6239 /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = "<group>"; };
+               A7E9B6B512D37EC400DA6239 /* consensus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensus.cpp; sourceTree = "<group>"; };
+               A7E9B6B612D37EC400DA6239 /* consensus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensus.h; sourceTree = "<group>"; };
                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensusseqscommand.cpp; sourceTree = "<group>"; };
                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensusseqscommand.h; sourceTree = "<group>"; };
                A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = corraxescommand.cpp; sourceTree = "<group>"; };
                A7E9B78612D37EC400DA6239 /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
                A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcoacommand.cpp; sourceTree = "<group>"; };
                A7E9B78812D37EC400DA6239 /* pcoacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcoacommand.h; sourceTree = "<group>"; };
-               A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
-               A7E9B78A12D37EC400DA6239 /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
                A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
                A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = "<group>"; };
                A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
                A7E9B7B312D37EC400DA6239 /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = "<group>"; };
                A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = "<group>"; };
                A7E9B7B512D37EC400DA6239 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
-               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
-               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
                A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
-               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
-               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
                A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
                A7E9B7BE12D37EC400DA6239 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
                A7E9B7BF12D37EC400DA6239 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
                A7E9B7C012D37EC400DA6239 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
-               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
-               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = "<group>"; };
                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = "<group>"; };
                A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = "<group>"; };
                                A7DAAFA3133A254E003956EB /* commandparameter.h */,
                                A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
                                A7E9BA4212D3960D00DA6239 /* containers */,
+                               A7E9B6B612D37EC400DA6239 /* consensus.h */,
+                               A7E9B6B512D37EC400DA6239 /* consensus.cpp */,
                                A7AACFBA132FE008003D6C4D /* currentfile.h */,
                                A7E9B6C912D37EC400DA6239 /* display.h */,
                                A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */,
                                A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
                                A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
                                A7E9B83112D37EC400DA6239 /* slibshuff.h */,
+                               A7876A28152A018B00A0AE86 /* subsample.h */,
+                               A7876A25152A017C00A0AE86 /* subsample.cpp */,
                                A7C3DC0E14FE469500FE1924 /* trialswap2.h */,
                                A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */,
                                A7FF19F0140FFDA500AD216D /* trimoligos.h */,
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76FB20486AB0100D96B5E /* Mothur */,
+                               8DD76FB20486AB0100D96B5E /* mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                };
-               A74D3644137DA7CE00332B0C /* uchime */ = {
-                       isa = PBXGroup;
-                       children = (
-                               A74D3655137DAB8300332B0C /* addtargets2.cpp */,
-                               A74D3656137DAB8300332B0C /* alignchime.cpp */,
-                               A74D3657137DAB8300332B0C /* alignchimel.cpp */,
-                               A74D3658137DAB8300332B0C /* allocs.h */,
-                               A74D3659137DAB8300332B0C /* alnheuristics.h */,
-                               A74D365A137DAB8300332B0C /* alnparams.cpp */,
-                               A74D365B137DAB8300332B0C /* alnparams.h */,
-                               A74D365C137DAB8300332B0C /* alpha.cpp */,
-                               A74D365D137DAB8300332B0C /* alpha.h */,
-                               A74D365E137DAB8300332B0C /* alpha2.cpp */,
-                               A74D365F137DAB8300332B0C /* chainer.h */,
-                               A74D3660137DAB8300332B0C /* chime.h */,
-                               A74D3661137DAB8300332B0C /* diagbox.h */,
-                               A74D3662137DAB8300332B0C /* dp.h */,
-                               A74D3663137DAB8300332B0C /* evalue.h */,
-                               A74D3664137DAB8300332B0C /* fractid.cpp */,
-                               A74D3665137DAB8300332B0C /* getparents.cpp */,
-                               A74D3666137DAB8300332B0C /* globalalign2.cpp */,
-                               A74D3667137DAB8300332B0C /* help.h */,
-                               A74D3668137DAB8300332B0C /* hsp.h */,
-                               A74D3669137DAB8300332B0C /* hspfinder.h */,
-                               A74D366A137DAB8300332B0C /* make3way.cpp */,
-                               A74D366B137DAB8300332B0C /* mx.cpp */,
-                               A74D366C137DAB8300332B0C /* mx.h */,
-                               A74D366D137DAB8300332B0C /* myopts.h */,
-                               A74D366E137DAB8300332B0C /* myutils.cpp */,
-                               A74D366F137DAB8300332B0C /* myutils.h */,
-                               A74D3670137DAB8300332B0C /* orf.h */,
-                               A74D3671137DAB8300332B0C /* out.h */,
-                               A74D3672137DAB8300332B0C /* path.cpp */,
-                               A74D3673137DAB8300332B0C /* path.h */,
-                               A74D3674137DAB8300332B0C /* searchchime.cpp */,
-                               A74D3675137DAB8300332B0C /* seq.h */,
-                               A74D3676137DAB8300332B0C /* seqdb.cpp */,
-                               A74D3677137DAB8300332B0C /* seqdb.h */,
-                               A74D3678137DAB8300332B0C /* setnucmx.cpp */,
-                               A74D3679137DAB8300332B0C /* sfasta.cpp */,
-                               A74D367A137DAB8300332B0C /* sfasta.h */,
-                               A74D367B137DAB8300332B0C /* svnmods.h */,
-                               A74D367C137DAB8300332B0C /* svnversion.h */,
-                               A74D367D137DAB8300332B0C /* timers.h */,
-                               A74D367E137DAB8300332B0C /* timing.h */,
-                               A74D367F137DAB8300332B0C /* tracebackbit.cpp */,
-                               A74D3680137DAB8300332B0C /* uc.h */,
-                               A74D3681137DAB8300332B0C /* uchime_main.cpp */,
-                               A74D3682137DAB8300332B0C /* ultra.h */,
-                               A74D3683137DAB8300332B0C /* usort.cpp */,
-                               A74D3684137DAB8300332B0C /* viterbifast.cpp */,
-                               A74D3685137DAB8300332B0C /* windex.h */,
-                               A74D3686137DAB8300332B0C /* writechhit.cpp */,
-                       );
-                       name = uchime;
-                       sourceTree = "<group>";
-               };
                A7D161E7149F7F50000523E8 /* fortran */ = {
                        isa = PBXGroup;
                        children = (
                        isa = PBXGroup;
                        children = (
                                A7E9B6AE12D37EC400DA6239 /* command.hpp */,
+                               219C1DE11552C508004209F9 /* newcommandtemplate.h */,
+                               219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */,
                                A7E9B65212D37EC300DA6239 /* aligncommand.h */,
                                A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
                                A7A61F2B130062E000E05B6B /* amovacommand.h */,
                                A71CB15E130B04A2001E7287 /* anosimcommand.cpp */,
                                A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
                                A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
-                               A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */,
-                               A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
                                A7E9B67312D37EC400DA6239 /* catchallcommand.h */,
                                A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
                                A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */,
                                A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */,
                                A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */,
                                A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */,
-                               A7E9B6B612D37EC400DA6239 /* consensuscommand.h */,
-                               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */,
                                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */,
                                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
                                A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */,
                                A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
                                A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */,
                                A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */,
+                               219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */,
+                               219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */,
                                A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
                                A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
                                A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
                                A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
                                A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */,
                                A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
+                               A70056E8156A93E300924A2D /* getotulabelscommand.h */,
+                               A70056E5156A93D000924A2D /* getotulabelscommand.cpp */,
                                A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */,
                                A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
                                A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */,
                                A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
                                A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
                                A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
+                               A7A0671C156294810095C8C5 /* listotulabelscommand.h */,
+                               A7A067191562946F0095C8C5 /* listotulabelscommand.cpp */,
                                A7E9B73E12D37EC400DA6239 /* listseqscommand.h */,
                                A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
+                               A73901051588C3EF00ED2ED6 /* loadlogfilecommand.h */,
+                               A73901071588C40900ED2ED6 /* loadlogfilecommand.cpp */,
                                A7FA10001302E096003860FE /* mantelcommand.h */,
                                A7FA10011302E096003860FE /* mantelcommand.cpp */,
+                               A724D2B4153C8600000A826F /* makebiomcommand.h */,
+                               A724D2B6153C8628000A826F /* makebiomcommand.cpp */,
+                               A7A0671D1562AC230095C8C5 /* makecontigscommand.h */,
+                               A7A0671E1562AC3E0095C8C5 /* makecontigscommand.cpp */,
                                A799F5B71309A3E000AEEFA0 /* makefastqcommand.h */,
                                A799F5B81309A3E000AEEFA0 /* makefastqcommand.cpp */,
                                A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
                                A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
                                A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
                                A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
-                               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */,
-                               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */,
-                               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */,
-                               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */,
-                               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */,
-                               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */,
                                A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
                                A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
                                A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
                                A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */,
                                A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
                                A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
+                               A70056E9156AB6D400924A2D /* removeotulabelscommand.h */,
+                               A70056EA156AB6E500924A2D /* removeotulabelscommand.cpp */,
                                A727864212E9E28C00F86ABA /* removerarecommand.h */,
                                A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
                                A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
                A7E9BA4512D3965600DA6239 /* chimera */ = {
                        isa = PBXGroup;
                        children = (
-                               A74D3644137DA7CE00332B0C /* uchime */,
                                A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */,
                                A7E9B65D12D37EC300DA6239 /* bellerophon.h */,
                                A7E9B67412D37EC400DA6239 /* ccode.cpp */,
                                A7E9B68F12D37EC400DA6239 /* classify.h */,
                                A7E9B73812D37EC400DA6239 /* knn.h */,
                                A7E9B73712D37EC400DA6239 /* knn.cpp */,
-                               A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */,
-                               A7E9B78A12D37EC400DA6239 /* phylodiversity.h */,
                                A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */,
                                A7E9B78E12D37EC400DA6239 /* phylosummary.h */,
                                A7E9B78F12D37EC400DA6239 /* phylotree.cpp */,
                                A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
                                A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
                                A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
+                               A7D755D71535F665009BF21A /* treereader.h */,
+                               A7D755D91535F679009BF21A /* treereader.cpp */,
                        );
                        name = read;
                        sourceTree = "<group>";
                        name = Mothur;
                        productInstallPath = "$(HOME)/bin";
                        productName = mothur;
-                       productReference = 8DD76FB20486AB0100D96B5E /* Mothur */;
+                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
                        attributes = {
+                               LastUpgradeCheck = 0420;
                                ORGANIZATIONNAME = "Schloss Lab";
                        };
                        buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
-                       compatibilityVersion = "Xcode 3.1";
+                       compatibilityVersion = "Xcode 3.2";
                        developmentRegion = English;
                        hasScannedForEncodings = 1;
                        knownRegions = (
                                A7E9B88C12D37EC400DA6239 /* blastdb.cpp in Sources */,
                                A7E9B88D12D37EC400DA6239 /* boneh.cpp in Sources */,
                                A7E9B88E12D37EC400DA6239 /* bootstrap.cpp in Sources */,
-                               A7E9B88F12D37EC400DA6239 /* bootstrapsharedcommand.cpp in Sources */,
                                A7E9B89012D37EC400DA6239 /* bstick.cpp in Sources */,
                                A7E9B89112D37EC400DA6239 /* calculator.cpp in Sources */,
                                A7E9B89212D37EC400DA6239 /* canberra.cpp in Sources */,
                                A7E9B8B012D37EC400DA6239 /* commandfactory.cpp in Sources */,
                                A7E9B8B112D37EC400DA6239 /* commandoptionparser.cpp in Sources */,
                                A7E9B8B212D37EC400DA6239 /* completelinkage.cpp in Sources */,
-                               A7E9B8B312D37EC400DA6239 /* consensuscommand.cpp in Sources */,
+                               A7E9B8B312D37EC400DA6239 /* consensus.cpp in Sources */,
                                A7E9B8B412D37EC400DA6239 /* consensusseqscommand.cpp in Sources */,
                                A7E9B8B512D37EC400DA6239 /* corraxescommand.cpp in Sources */,
                                A7E9B8B612D37EC400DA6239 /* coverage.cpp in Sources */,
                                A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */,
                                A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
                                A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */,
-                               A7E9B91612D37EC400DA6239 /* phylodiversity.cpp in Sources */,
                                A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */,
                                A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */,
                                A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */,
                                A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */,
                                A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */,
                                A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */,
-                               A7E9B92C12D37EC400DA6239 /* readdistcommand.cpp in Sources */,
-                               A7E9B92E12D37EC400DA6239 /* readotucommand.cpp in Sources */,
                                A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */,
                                A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */,
-                               A7E9B93112D37EC400DA6239 /* readtreecommand.cpp in Sources */,
                                A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */,
                                A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */,
                                A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */,
                                A7FE7C401330EA1000F7B327 /* getcurrentcommand.cpp in Sources */,
                                A7FE7E6D13311EA400F7B327 /* setcurrentcommand.cpp in Sources */,
                                A778FE6B134CA6CA00C0BA33 /* getcommandinfocommand.cpp in Sources */,
-                               A74D3687137DAB8300332B0C /* addtargets2.cpp in Sources */,
-                               A74D3688137DAB8400332B0C /* alignchime.cpp in Sources */,
-                               A74D3689137DAB8400332B0C /* alignchimel.cpp in Sources */,
-                               A74D368A137DAB8400332B0C /* alnparams.cpp in Sources */,
-                               A74D368B137DAB8400332B0C /* alpha.cpp in Sources */,
-                               A74D368C137DAB8400332B0C /* alpha2.cpp in Sources */,
-                               A74D368D137DAB8400332B0C /* fractid.cpp in Sources */,
-                               A74D368E137DAB8400332B0C /* getparents.cpp in Sources */,
-                               A74D368F137DAB8400332B0C /* globalalign2.cpp in Sources */,
-                               A74D3690137DAB8400332B0C /* make3way.cpp in Sources */,
-                               A74D3691137DAB8400332B0C /* mx.cpp in Sources */,
-                               A74D3692137DAB8400332B0C /* myutils.cpp in Sources */,
-                               A74D3693137DAB8400332B0C /* path.cpp in Sources */,
-                               A74D3694137DAB8400332B0C /* searchchime.cpp in Sources */,
-                               A74D3695137DAB8400332B0C /* seqdb.cpp in Sources */,
-                               A74D3696137DAB8400332B0C /* setnucmx.cpp in Sources */,
-                               A74D3697137DAB8400332B0C /* sfasta.cpp in Sources */,
-                               A74D3698137DAB8400332B0C /* tracebackbit.cpp in Sources */,
-                               A74D3699137DAB8400332B0C /* uchime_main.cpp in Sources */,
-                               A74D369A137DAB8400332B0C /* usort.cpp in Sources */,
-                               A74D369B137DAB8400332B0C /* viterbifast.cpp in Sources */,
-                               A74D369C137DAB8400332B0C /* writechhit.cpp in Sources */,
                                A74D36B8137DAFAA00332B0C /* chimerauchimecommand.cpp in Sources */,
                                A77A221F139001B600B0BE70 /* deuniquetreecommand.cpp in Sources */,
                                A7730EFF13967241007433A3 /* countseqscommand.cpp in Sources */,
                                A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */,
                                A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */,
                                A77EBD2F1523709100ED407C /* createdatabasecommand.cpp in Sources */,
+                               A7876A26152A017C00A0AE86 /* subsample.cpp in Sources */,
+                               A7D755DA1535F679009BF21A /* treereader.cpp in Sources */,
+                               A724D2B7153C8628000A826F /* makebiomcommand.cpp in Sources */,
+                               219C1DE01552C4BD004209F9 /* newcommandtemplate.cpp in Sources */,
+                               219C1DE41559BCCF004209F9 /* getcoremicrobiomecommand.cpp in Sources */,
+                               A7A0671A1562946F0095C8C5 /* listotulabelscommand.cpp in Sources */,
+                               A7A0671F1562AC3E0095C8C5 /* makecontigscommand.cpp in Sources */,
+                               A70056E6156A93D000924A2D /* getotulabelscommand.cpp in Sources */,
+                               A70056EB156AB6E500924A2D /* removeotulabelscommand.cpp in Sources */,
+                               A73901081588C40900ED2ED6 /* loadlogfilecommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                        buildSettings = {
                                ALWAYS_SEARCH_USER_PATHS = NO;
                                COPY_PHASE_STRIP = NO;
+                               DEPLOYMENT_LOCATION = YES;
                                GCC_DYNAMIC_NO_PIC = NO;
-                               GCC_ENABLE_FIX_AND_CONTINUE = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_OPTIMIZATION_LEVEL = 0;
-                               INSTALL_PATH = /usr/local/bin;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                        };
                        name = Debug;
                };
                                DEPLOYMENT_LOCATION = YES;
                                GCC_MODEL_TUNING = G5;
                                GCC_WARN_UNUSED_VALUE = YES;
-                               INSTALL_PATH = ./;
-                               PRODUCT_NAME = Mothur;
+                               PRODUCT_NAME = mothur;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.24.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
+                                       "VERSION=\"\\\"1.25.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/01/2012\\\"\"",
                                );
                                "GCC_VERSION[arch=*]" = "";
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
                                HEADER_SEARCH_PATHS = "";
-                               INSTALL_PATH = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               PREBINDING = NO;
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                                USER_HEADER_SEARCH_PATHS = "";
                        };
                        name = Debug;
                                GCC_MODEL_TUNING = "";
                                GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "VERSION=\"\\\"1.24.0\\\"\"",
-                                       "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
+                                       "VERSION=\"\\\"1.25.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"4/30/2012\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_PARAMETER = YES;
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               INSTALL_PATH = "";
+                               INSTALL_PATH = TARGET_BUILD_DIR;
                                MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
                                        "-DUSE_READLINE",
                                        "-lncurses",
                                        "-lreadline",
                                );
-                               PREBINDING = NO;
                                SDKROOT = macosx10.6;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };