]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added pcr.seqs command. fixed bug in rarefacftion.single that caused parsing error...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index d3b9cfc04051882ed9f2260dfd5143b6192714c9..2550873ae612a60d93d937c21908389e515a306b 100644 (file)
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                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>"; };
                8DD76FB20486AB0100D96B5E /* Mothur */ = {isa = PBXFileReference; explicitFileType = "compiled.mach-o.executable"; includeInIndex = 0; path = Mothur; sourceTree = BUILT_PRODUCTS_DIR; };
                A70332B512D3A13400761E33 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
                A713EBAA12DC7613000092AC /* readphylipvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylipvector.h; sourceTree = "<group>"; };
                A71CB15F130B04A2001E7287 /* anosimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = anosimcommand.h; sourceTree = "<group>"; };
                A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergegroupscommand.h; 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>"; };
                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>"; };
+               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>"; };
+               A74D3657137DAB8300332B0C /* alignchimel.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alignchimel.cpp; sourceTree = "<group>"; };
+               A74D3658137DAB8300332B0C /* allocs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = allocs.h; sourceTree = "<group>"; };
+               A74D3659137DAB8300332B0C /* alnheuristics.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alnheuristics.h; sourceTree = "<group>"; };
+               A74D365A137DAB8300332B0C /* alnparams.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alnparams.cpp; sourceTree = "<group>"; };
+               A74D365B137DAB8300332B0C /* alnparams.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alnparams.h; sourceTree = "<group>"; };
+               A74D365C137DAB8300332B0C /* alpha.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alpha.cpp; sourceTree = "<group>"; };
+               A74D365D137DAB8300332B0C /* alpha.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = alpha.h; sourceTree = "<group>"; };
+               A74D365E137DAB8300332B0C /* alpha2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = alpha2.cpp; sourceTree = "<group>"; };
+               A74D365F137DAB8300332B0C /* chainer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chainer.h; sourceTree = "<group>"; };
+               A74D3660137DAB8300332B0C /* chime.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chime.h; sourceTree = "<group>"; };
+               A74D3661137DAB8300332B0C /* diagbox.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = diagbox.h; sourceTree = "<group>"; };
+               A74D3662137DAB8300332B0C /* dp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dp.h; sourceTree = "<group>"; };
+               A74D3663137DAB8300332B0C /* evalue.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = evalue.h; sourceTree = "<group>"; };
+               A74D3664137DAB8300332B0C /* fractid.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fractid.cpp; sourceTree = "<group>"; };
+               A74D3665137DAB8300332B0C /* getparents.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getparents.cpp; sourceTree = "<group>"; };
+               A74D3666137DAB8300332B0C /* globalalign2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globalalign2.cpp; sourceTree = "<group>"; };
+               A74D3667137DAB8300332B0C /* help.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = help.h; sourceTree = "<group>"; };
+               A74D3668137DAB8300332B0C /* hsp.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hsp.h; sourceTree = "<group>"; };
+               A74D3669137DAB8300332B0C /* hspfinder.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hspfinder.h; sourceTree = "<group>"; };
+               A74D366A137DAB8300332B0C /* make3way.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = make3way.cpp; sourceTree = "<group>"; };
+               A74D366B137DAB8300332B0C /* mx.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mx.cpp; sourceTree = "<group>"; };
+               A74D366C137DAB8300332B0C /* mx.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mx.h; sourceTree = "<group>"; };
+               A74D366D137DAB8300332B0C /* myopts.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myopts.h; sourceTree = "<group>"; };
+               A74D366E137DAB8300332B0C /* myutils.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = myutils.cpp; sourceTree = "<group>"; };
+               A74D366F137DAB8300332B0C /* myutils.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = myutils.h; sourceTree = "<group>"; };
+               A74D3670137DAB8300332B0C /* orf.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = orf.h; sourceTree = "<group>"; };
+               A74D3671137DAB8300332B0C /* out.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = out.h; sourceTree = "<group>"; };
+               A74D3672137DAB8300332B0C /* path.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = path.cpp; sourceTree = "<group>"; };
+               A74D3673137DAB8300332B0C /* path.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = path.h; sourceTree = "<group>"; };
+               A74D3674137DAB8300332B0C /* searchchime.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = searchchime.cpp; sourceTree = "<group>"; };
+               A74D3675137DAB8300332B0C /* seq.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seq.h; sourceTree = "<group>"; };
+               A74D3676137DAB8300332B0C /* seqdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqdb.cpp; sourceTree = "<group>"; };
+               A74D3677137DAB8300332B0C /* seqdb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqdb.h; sourceTree = "<group>"; };
+               A74D3678137DAB8300332B0C /* setnucmx.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setnucmx.cpp; sourceTree = "<group>"; };
+               A74D3679137DAB8300332B0C /* sfasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sfasta.cpp; sourceTree = "<group>"; };
+               A74D367A137DAB8300332B0C /* sfasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sfasta.h; sourceTree = "<group>"; };
+               A74D367B137DAB8300332B0C /* svnmods.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = svnmods.h; sourceTree = "<group>"; };
+               A74D367C137DAB8300332B0C /* svnversion.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = svnversion.h; sourceTree = "<group>"; };
+               A74D367D137DAB8300332B0C /* timers.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = timers.h; sourceTree = "<group>"; };
+               A74D367E137DAB8300332B0C /* timing.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = timing.h; sourceTree = "<group>"; };
+               A74D367F137DAB8300332B0C /* tracebackbit.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tracebackbit.cpp; sourceTree = "<group>"; };
+               A74D3680137DAB8300332B0C /* uc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uc.h; sourceTree = "<group>"; };
+               A74D3681137DAB8300332B0C /* uchime_main.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uchime_main.cpp; sourceTree = "<group>"; };
+               A74D3682137DAB8300332B0C /* ultra.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ultra.h; sourceTree = "<group>"; };
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+               A74D3684137DAB8300332B0C /* viterbifast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = viterbifast.cpp; sourceTree = "<group>"; };
+               A74D3685137DAB8300332B0C /* windex.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = windex.h; sourceTree = "<group>"; };
+               A74D3686137DAB8300332B0C /* writechhit.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = writechhit.cpp; sourceTree = "<group>"; };
+               A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerauchimecommand.h; sourceTree = "<group>"; };
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                A75790581301749D00A30DAB /* homovacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = homovacommand.cpp; sourceTree = "<group>"; };
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+               A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuassociationcommand.cpp; sourceTree = "<group>"; };
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                A7A61F2B130062E000E05B6B /* amovacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = amovacommand.h; sourceTree = "<group>"; };
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                A7E9B6E712D37EC400DA6239 /* flowdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = flowdata.cpp; sourceTree = "<group>"; };
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                A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = "<group>"; };
                A7E9B75412D37EC400DA6239 /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = "<group>"; };
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                A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = "<group>"; };
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                A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = "<group>"; };
                A7E9B7E812D37EC400DA6239 /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = "<group>"; };
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                A7E9B7EA12D37EC400DA6239 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
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                A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = "<group>"; };
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                A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
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                A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = "<group>"; };
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                A7E9B85712D37EC400DA6239 /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = "<group>"; };
                A7E9B85812D37EC400DA6239 /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = "<group>"; };
                A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
                A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = SOURCE_ROOT; };
                A7E9B87F12D37EC400DA6239 /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
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                A7FA10011302E096003860FE /* mantelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mantelcommand.cpp; sourceTree = "<group>"; };
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                A7FC480D12D788F20055BC5C /* linearalgebra.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = linearalgebra.cpp; sourceTree = "<group>"; };
                A7FC486512D795D60055BC5C /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = "<group>"; };
                A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getcurrentcommand.cpp; sourceTree = "<group>"; };
                A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setcurrentcommand.h; sourceTree = "<group>"; };
                A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setcurrentcommand.cpp; sourceTree = "<group>"; };
+               A7FF19F0140FFDA500AD216D /* trimoligos.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimoligos.h; sourceTree = "<group>"; };
+               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimoligos.cpp; sourceTree = "<group>"; };
+               A7FFB556142CA02C004884F2 /* summarytaxcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarytaxcommand.h; sourceTree = "<group>"; };
+               A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarytaxcommand.cpp; sourceTree = "<group>"; };
                C6A0FF2C0290799A04C91782 /* mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = mothur.1; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
                                A7E9B75C12D37EC400DA6239 /* mothur.h */,
                                A7E9B75D12D37EC400DA6239 /* mothurout.cpp */,
                                A7E9B75E12D37EC400DA6239 /* mothurout.h */,
+                               A774104714696F320098E6AC /* myseqdist.h */,
+                               A774104614696F320098E6AC /* myseqdist.cpp */,
                                A7E9B76112D37EC400DA6239 /* nast.cpp */,
                                A7E9B76212D37EC400DA6239 /* nast.hpp */,
                                A7E9B76312D37EC400DA6239 /* nastreport.cpp */,
                                A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */,
                                7E6BE10812F710D8007ADDBE /* refchimeratest.h */,
                                7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */,
+                               A77410F514697C300098E6AC /* seqnoise.h */,
+                               A77410F414697C300098E6AC /* seqnoise.cpp */,
                                A7E9BA5312D39A5E00DA6239 /* read */,
                                A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */,
                                A7E9B82412D37EC400DA6239 /* sharedutilities.h */,
                                A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
                                A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
-                               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
                                A7E9B83112D37EC400DA6239 /* slibshuff.h */,
-                               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
-                               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
-                               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
-                               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
-                               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
+                               A7C3DC0E14FE469500FE1924 /* trialswap2.h */,
+                               A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */,
+                               A7FF19F0140FFDA500AD216D /* trimoligos.h */,
+                               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */,
                                A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
                                A7E9B87512D37EC400DA6239 /* validcalculator.h */,
                                A7E9B87612D37EC400DA6239 /* validparameter.cpp */,
                        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 = (
+                               A7FA2B5A14A0F0C2007C09A6 /* intrv.f */,
+                               A7FA2B1514A0EBEA007C09A6 /* sslvrg.f */,
+                               A7FA2ABC14A0E881007C09A6 /* bsplvb.f */,
+                               A7FA2ABD14A0E881007C09A6 /* bsplvd.f */,
+                               A7FA2ABE14A0E881007C09A6 /* bvalue.f */,
+                               A7FA2ABF14A0E881007C09A6 /* daxpy.f */,
+                               A7FA2AC014A0E881007C09A6 /* ddot.f */,
+                               A7FA2AC114A0E881007C09A6 /* dpbfa.f */,
+                               A7FA2AC214A0E881007C09A6 /* dpbsl.f */,
+                               A7FA2AC314A0E881007C09A6 /* interv.f */,
+                               A7FA2AC414A0E881007C09A6 /* sgram.f */,
+                               A7FA2AC514A0E881007C09A6 /* sinerp.f */,
+                               A7FA2AC614A0E881007C09A6 /* stxwx.f */,
+                       );
+                       name = fortran;
+                       sourceTree = "<group>";
+               };
                A7E9BA3812D3956100DA6239 /* commands */ = {
                        isa = PBXGroup;
                        children = (
                                A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */,
                                A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */,
                                A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */,
+                               A7BF2230145879B2000AD524 /* chimeraperseuscommand.h */,
+                               A7BF2231145879B2000AD524 /* chimeraperseuscommand.cpp */,
                                A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */,
                                A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */,
+                               A74D36B6137DAFAA00332B0C /* chimerauchimecommand.h */,
+                               A74D36B7137DAFAA00332B0C /* chimerauchimecommand.cpp */,
                                A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */,
                                A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */,
                                A7E9B69112D37EC400DA6239 /* classifyotucommand.h */,
                                A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */,
                                A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */,
                                A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
+                               A7EEB0F714F29C1B00344B83 /* classifytreecommand.h */,
+                               A7EEB0F414F29BFD00344B83 /* classifytreecommand.cpp */,
                                A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
                                A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */,
+                               A73DDBB813C4A0D1006AAE38 /* clearmemorycommand.h */,
+                               A73DDBB913C4A0D1006AAE38 /* clearmemorycommand.cpp */,
                                A7E9B69D12D37EC400DA6239 /* clustercommand.h */,
                                A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */,
                                A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */,
                                A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */,
                                A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */,
                                A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
+                               A7C3DC0A14FE457500FE1924 /* cooccurrencecommand.h */,
+                               A7C3DC0914FE457500FE1924 /* cooccurrencecommand.cpp */,
                                A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
                                A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+                               A795840B13F13CD900F201D5 /* countgroupscommand.h */,
+                               A795840C13F13CD900F201D5 /* countgroupscommand.cpp */,
+                               A7730EFD13967241007433A3 /* countseqscommand.h */,
+                               A7730EFE13967241007433A3 /* countseqscommand.cpp */,
                                A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
                                A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
                                A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */,
                                A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */,
                                A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */,
                                A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */,
+                               A77A221D139001B600B0BE70 /* deuniquetreecommand.h */,
+                               A77A221E139001B600B0BE70 /* deuniquetreecommand.cpp */,
                                A7E9B6CC12D37EC400DA6239 /* distancecommand.h */,
                                A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
                                A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
                                A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
                                A713EBEB12DC7C5E000092AC /* nmdscommand.h */,
                                A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */,
+                               A7A3C8C814D041AD00B1BFBE /* otuassociationcommand.h */,
+                               A7A3C8C714D041AD00B1BFBE /* otuassociationcommand.cpp */,
                                A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */,
                                A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */,
                                A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */,
                                A7FC486612D795D60055BC5C /* pcacommand.cpp */,
                                A7E9B78812D37EC400DA6239 /* pcoacommand.h */,
                                A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
+                               A76CDD7F1510F09A004C8458 /* pcrseqscommand.h */,
+                               A76CDD811510F143004C8458 /* prcseqscommand.cpp */,
                                A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */,
                                A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
                                A7E9B79212D37EC400DA6239 /* phylotypecommand.h */,
                                A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
                                A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
                                A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */,
+                               A774101214695AF60098E6AC /* shhhseqscommand.h */,
+                               A774101314695AF60098E6AC /* shhhseqscommand.cpp */,
+                               A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */,
+                               A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */,
                                A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
                                A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
                                A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
                                A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */,
                                A7E9B85812D37EC400DA6239 /* summarycommand.h */,
                                A7E9B85712D37EC400DA6239 /* summarycommand.cpp */,
+                               A754149514840CF7005850D1 /* summaryqualcommand.h */,
+                               A754149614840CF7005850D1 /* summaryqualcommand.cpp */,
                                A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */,
                                A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
+                               A7FFB556142CA02C004884F2 /* summarytaxcommand.h */,
+                               A7FFB557142CA02C004884F2 /* summarytaxcommand.cpp */,
                                A7E9B85C12D37EC400DA6239 /* systemcommand.h */,
                                A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */,
                                A7E9B86312D37EC400DA6239 /* treegroupscommand.h */,
                A7E9BA3F12D395F700DA6239 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
+                               7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */,
                                A7E9B64F12D37EC300DA6239 /* ace.cpp */,
                                A7E9B65012D37EC300DA6239 /* ace.h */,
                                A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */,
                                A7E9B6D712D37EC400DA6239 /* efron.cpp */,
                                A7E9B6D812D37EC400DA6239 /* efron.h */,
                                A7E9B6E212D37EC400DA6239 /* filters.h */,
-                               A7E9B6E512D37EC400DA6239 /* fisher2.c */,
-                               A7E9B6E612D37EC400DA6239 /* fisher2.h */,
                                A7E9B6F012D37EC400DA6239 /* geom.cpp */,
                                A7E9B6F112D37EC400DA6239 /* geom.h */,
                                A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */,
                                A7E9B7E812D37EC400DA6239 /* shannoneven.h */,
                                A7E9B7E912D37EC400DA6239 /* sharedace.cpp */,
                                A7E9B7EA12D37EC400DA6239 /* sharedace.h */,
-                               A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */,
                                A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */,
                                A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */,
                                A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */,
                                A7E9B7A012D37EC400DA6239 /* qualityscores.h */,
                                A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */,
                                A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */,
+                               A721765513BB9F7D0014DAAE /* referencedb.h */,
+                               A721765613BB9F7D0014DAAE /* referencedb.cpp */,
                                A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */,
                                A7E9B7CC12D37EC400DA6239 /* reportfile.h */,
                                A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */,
                                A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
                                A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
                                A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
+                               A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
+                               A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */,
                                A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */,
                                A7E9B80512D37EC400DA6239 /* sharedlistvector.h */,
                                A7E9B80E12D37EC400DA6239 /* sharedordervector.h */,
                                A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
-                               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
                                A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */,
+                               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
                                A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */,
                                A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */,
                                A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */,
                                A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
                                A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
                                A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
+                               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
+                               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
+                               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
+                               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
+                               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
                                A7E9B85F12D37EC400DA6239 /* tree.cpp */,
                                A7E9B86012D37EC400DA6239 /* tree.h */,
                                A7E9B86412D37EC400DA6239 /* treemap.cpp */,
                A7E9BA4512D3965600DA6239 /* chimera */ = {
                        isa = PBXGroup;
                        children = (
+                               A74D3644137DA7CE00332B0C /* uchime */,
                                A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */,
                                A7E9B65D12D37EC300DA6239 /* bellerophon.h */,
                                A7E9B67412D37EC400DA6239 /* ccode.cpp */,
                                A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */,
                                A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */,
                                A7E9B68512D37EC400DA6239 /* chimerarealigner.h */,
+                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
+                               A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
                                A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */,
                                A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
-                               A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
                                A7E9B74612D37EC400DA6239 /* maligner.h */,
-                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
                                A7E9B74512D37EC400DA6239 /* maligner.cpp */,
+                               A7BF221314587886000AD524 /* myPerseus.h */,
+                               A7BF221214587886000AD524 /* myPerseus.cpp */,
                                A7E9B79312D37EC400DA6239 /* pintail.cpp */,
                                A7E9B79412D37EC400DA6239 /* pintail.h */,
                                A7E9B82E12D37EC400DA6239 /* slayer.cpp */,
                A7E9BA5612D39BD800DA6239 /* metastats */ = {
                        isa = PBXGroup;
                        children = (
-                               A7E9B75512D37EC400DA6239 /* metastats.h */,
-                               A7E9B75612D37EC400DA6239 /* metastats2.c */,
+                               A7D161E7149F7F50000523E8 /* fortran */,
+                               A79234D513C74BF6002B08E2 /* mothurfisher.h */,
+                               A79234D613C74BF6002B08E2 /* mothurfisher.cpp */,
+                               A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */,
+                               A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */,
+                               A74A9A9D148E881E00AB5E3E /* spline.h */,
+                               A74A9A9E148E881E00AB5E3E /* spline.cpp */,
                        );
                        name = metastats;
                        sourceTree = "<group>";
                                8DD76FAF0486AB0100D96B5E /* CopyFiles */,
                        );
                        buildRules = (
+                               A7D162CB149F96CA000523E8 /* PBXBuildRule */,
                        );
                        dependencies = (
                        );
                                A7E9B8C412D37EC400DA6239 /* fastamap.cpp in Sources */,
                                A7E9B8C512D37EC400DA6239 /* fileoutput.cpp in Sources */,
                                A7E9B8C612D37EC400DA6239 /* filterseqscommand.cpp in Sources */,
-                               A7E9B8C712D37EC400DA6239 /* fisher2.c in Sources */,
                                A7E9B8C812D37EC400DA6239 /* flowdata.cpp in Sources */,
                                A7E9B8C912D37EC400DA6239 /* formatcolumn.cpp in Sources */,
                                A7E9B8CA12D37EC400DA6239 /* formatphylip.cpp in Sources */,
                                A7E9B8FB12D37EC400DA6239 /* memeuclidean.cpp in Sources */,
                                A7E9B8FC12D37EC400DA6239 /* mempearson.cpp in Sources */,
                                A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */,
-                               A7E9B8FE12D37EC400DA6239 /* metastats2.c in Sources */,
                                A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */,
                                A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */,
                                A7E9B90112D37EC400DA6239 /* mothur.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 */,
+                               A721765713BB9F7D0014DAAE /* referencedb.cpp in Sources */,
+                               A73DDBBA13C4A0D1006AAE38 /* clearmemorycommand.cpp in Sources */,
+                               A73DDC3813C4BF64006AAE38 /* mothurmetastats.cpp in Sources */,
+                               A79234D713C74BF6002B08E2 /* mothurfisher.cpp in Sources */,
+                               A795840D13F13CD900F201D5 /* countgroupscommand.cpp in Sources */,
+                               A7FF19F2140FFDA500AD216D /* trimoligos.cpp in Sources */,
+                               A7F9F5CF141A5E500032F693 /* sequenceparser.cpp in Sources */,
+                               A7FFB558142CA02C004884F2 /* summarytaxcommand.cpp in Sources */,
+                               A7BF221414587886000AD524 /* myPerseus.cpp in Sources */,
+                               A7BF2232145879B2000AD524 /* chimeraperseuscommand.cpp in Sources */,
+                               A774101414695AF60098E6AC /* shhhseqscommand.cpp in Sources */,
+                               A774104814696F320098E6AC /* myseqdist.cpp in Sources */,
+                               A77410F614697C300098E6AC /* seqnoise.cpp in Sources */,
+                               A754149714840CF7005850D1 /* summaryqualcommand.cpp in Sources */,
+                               A74A9A9F148E881E00AB5E3E /* spline.cpp in Sources */,
+                               A7FA2AC714A0E881007C09A6 /* bsplvb.f in Sources */,
+                               A7FA2AC814A0E881007C09A6 /* bsplvd.f in Sources */,
+                               A7FA2AC914A0E881007C09A6 /* bvalue.f in Sources */,
+                               A7FA2ACA14A0E881007C09A6 /* daxpy.f in Sources */,
+                               A7FA2ACB14A0E881007C09A6 /* ddot.f in Sources */,
+                               A7FA2ACC14A0E881007C09A6 /* dpbfa.f in Sources */,
+                               A7FA2ACD14A0E881007C09A6 /* dpbsl.f in Sources */,
+                               A7FA2ACE14A0E881007C09A6 /* interv.f in Sources */,
+                               A7FA2ACF14A0E881007C09A6 /* sgram.f in Sources */,
+                               A7FA2AD014A0E881007C09A6 /* sinerp.f in Sources */,
+                               A7FA2AD114A0E881007C09A6 /* stxwx.f in Sources */,
+                               A7FA2B1614A0EBEA007C09A6 /* sslvrg.f in Sources */,
+                               A7FA2B5B14A0F0C2007C09A6 /* intrv.f in Sources */,
+                               A7A3C8C914D041AD00B1BFBE /* otuassociationcommand.cpp in Sources */,
+                               A7A32DAA14DC43B00001D2E5 /* sortseqscommand.cpp in Sources */,
+                               A7EEB0F514F29BFE00344B83 /* classifytreecommand.cpp in Sources */,
+                               A7C3DC0B14FE457500FE1924 /* cooccurrencecommand.cpp in Sources */,
+                               A7C3DC0F14FE469500FE1924 /* trialSwap2.cpp in Sources */,
+                               A76CDD821510F143004C8458 /* prcseqscommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                ARCHS = "$(ARCHS_STANDARD_64_BIT)";
                                DEPLOYMENT_LOCATION = NO;
                                GCC_C_LANGUAGE_STANDARD = gnu99;
-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_ENABLE_SSE3_EXTENSIONS = NO;
+                               GCC_ENABLE_SSE41_EXTENSIONS = NO;
+                               GCC_ENABLE_SSE42_EXTENSIONS = NO;
+                               GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
                                        "MOTHUR_FILES=\"\\\"../release\\\"\"",
-                                       "VERSION=\"\\\"1.18.1\\\"\"",
-                                       "RELEASE_DATE=\"\\\"4/15/2011\\\"\"",
+                                       "VERSION=\"\\\"1.24.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
                                );
+                               "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 = "";
                                MACH_O_TYPE = mh_execute;
                                ONLY_ACTIVE_ARCH = YES;
                                );
                                PREBINDING = NO;
                                SDKROOT = macosx10.6;
+                               USER_HEADER_SEARCH_PATHS = "";
                        };
                        name = Debug;
                };
                                GCC_C_LANGUAGE_STANDARD = gnu99;
                                GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
                                GCC_MODEL_TUNING = "";
-                               GCC_OPTIMIZATION_LEVEL = 3;
+                               GCC_OPTIMIZATION_LEVEL = 0;
                                GCC_PREPROCESSOR_DEFINITIONS = (
-                                       "VERSION=\"\\\"1.18.1\\\"\"",
-                                       "RELEASE_DATE=\"\\\"4/15/2011\\\"\"",
+                                       "VERSION=\"\\\"1.24.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"3/12/2012\\\"\"",
                                );
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;