]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added rename.seqs command.
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 6aa6b2774a80080173293dc3af259e01952f1d49..77cfb8c6cd50b9ec16746ef64d16f142be6fb8dc 100644 (file)
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+               A7FA2AD114A0E881007C09A6 /* stxwx.f in Sources */ = {isa = PBXBuildFile; fileRef = A7FA2AC614A0E881007C09A6 /* stxwx.f */; };
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+               A7FC486712D795D60055BC5C /* pcacommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = A7FC486612D795D60055BC5C /* pcacommand.cpp */; };
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 /* End PBXBuildFile section */
 
+/* Begin PBXBuildRule section */
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+                       outputFiles = (
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+               };
+/* End PBXBuildRule section */
+
 /* Begin PBXCopyFilesBuildPhase section */
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                        buildActionMask = 8;
-                       dstPath = /usr/share/man/man1/;
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+                       dstPath = Users/SarahsWork/desktop/debug;
+                       dstSubfolderSpec = 16;
                        files = (
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+                               8DD76FB00486AB0100D96B5E /* mothur.1 in CopyFiles */,
                        );
                        runOnlyForDeploymentPostprocessing = 1;
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 /* Begin PBXFileReference section */
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+               A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = "<group>"; };
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+               A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = SOURCE_ROOT; };
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+               A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = consensusseqscommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
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+               A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = corraxescommand.cpp; sourceTree = "<group>"; };
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+               A7E9B6BB12D37EC400DA6239 /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = "<group>"; };
+               A7E9B6BC12D37EC400DA6239 /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = "<group>"; };
+               A7E9B6BD12D37EC400DA6239 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = "<group>"; };
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+               A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
+               A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
+               A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = degapseqscommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
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+               A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deuniqueseqscommand.cpp; sourceTree = "<group>"; };
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+               A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = distancecommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
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+               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = "<group>"; };
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+               A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = SOURCE_ROOT; };
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+               A7E9B6DF12D37EC400DA6239 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = "<group>"; };
+               A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = SOURCE_ROOT; };
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+               A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = "<group>"; };
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+               A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupscommand.cpp; sourceTree = "<group>"; };
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+               A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = "<group>"; };
+               A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = "<group>"; };
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+               A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = getsabundcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
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+               A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = "<group>"; };
+               A7E9B70912D37EC400DA6239 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = "<group>"; };
+               A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = "<group>"; };
+               A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = "<group>"; };
+               A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = "<group>"; };
+               A7E9B70F12D37EC400DA6239 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = "<group>"; };
+               A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = gotohoverlap.hpp; sourceTree = SOURCE_ROOT; };
+               A7E9B71212D37EC400DA6239 /* gower.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gower.cpp; sourceTree = "<group>"; };
+               A7E9B71312D37EC400DA6239 /* gower.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = gower.h; sourceTree = "<group>"; };
+               A7E9B71412D37EC400DA6239 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = "<group>"; };
+               A7E9B71512D37EC400DA6239 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = "<group>"; };
+               A7E9B71612D37EC400DA6239 /* hamming.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hamming.cpp; sourceTree = "<group>"; };
+               A7E9B71712D37EC400DA6239 /* hamming.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hamming.h; sourceTree = "<group>"; };
+               A7E9B71812D37EC400DA6239 /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B71912D37EC400DA6239 /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = SOURCE_ROOT; };
+               A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = "<group>"; };
+               A7E9B71B12D37EC400DA6239 /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = "<group>"; };
+               A7E9B71C12D37EC400DA6239 /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B71D12D37EC400DA6239 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = SOURCE_ROOT; };
+               A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = "<group>"; };
+               A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = "<group>"; };
+               A7E9B72012D37EC400DA6239 /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B72112D37EC400DA6239 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; };
+               A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = "<group>"; };
+               A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = "<group>"; };
+               A7E9B72412D37EC400DA6239 /* heip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heip.cpp; sourceTree = "<group>"; };
+               A7E9B72512D37EC400DA6239 /* heip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heip.h; sourceTree = "<group>"; };
+               A7E9B72612D37EC400DA6239 /* hellinger.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hellinger.cpp; sourceTree = "<group>"; };
+               A7E9B72712D37EC400DA6239 /* hellinger.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hellinger.h; sourceTree = "<group>"; };
+               A7E9B72812D37EC400DA6239 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = "<group>"; };
+               A7E9B72912D37EC400DA6239 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = "<group>"; };
+               A7E9B72A12D37EC400DA6239 /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = "<group>"; };
+               A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = indicatorcommand.cpp; sourceTree = "<group>"; };
+               A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = indicatorcommand.h; sourceTree = "<group>"; };
+               A7E9B72D12D37EC400DA6239 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B72E12D37EC400DA6239 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = SOURCE_ROOT; };
+               A7E9B72F12D37EC400DA6239 /* invsimpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = invsimpson.cpp; sourceTree = "<group>"; };
+               A7E9B73012D37EC400DA6239 /* invsimpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = invsimpson.h; sourceTree = "<group>"; };
+               A7E9B73112D37EC400DA6239 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = "<group>"; };
+               A7E9B73212D37EC400DA6239 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = "<group>"; };
+               A7E9B73312D37EC400DA6239 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = "<group>"; };
+               A7E9B73412D37EC400DA6239 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = "<group>"; };
+               A7E9B73512D37EC400DA6239 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = "<group>"; };
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+               A7E9B73712D37EC400DA6239 /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = "<group>"; };
+               A7E9B73812D37EC400DA6239 /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = "<group>"; };
+               A7E9B73912D37EC400DA6239 /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B73A12D37EC400DA6239 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = SOURCE_ROOT; };
+               A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = "<group>"; };
+               A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = "<group>"; };
+               A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = listseqscommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
+               A7E9B73E12D37EC400DA6239 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = "<group>"; };
+               A7E9B73F12D37EC400DA6239 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = "<group>"; };
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+               A7E9B74112D37EC400DA6239 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
+               A7E9B74212D37EC400DA6239 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
+               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; lineEnding = 0; path = makegroupcommand.cpp; sourceTree = "<group>"; xcLanguageSpecificationIdentifier = xcode.lang.cpp; };
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+               A7E9B74512D37EC400DA6239 /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = "<group>"; };
+               A7E9B74612D37EC400DA6239 /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = "<group>"; };
+               A7E9B74712D37EC400DA6239 /* manhattan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = manhattan.cpp; sourceTree = "<group>"; };
+               A7E9B74812D37EC400DA6239 /* manhattan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = manhattan.h; sourceTree = "<group>"; };
+               A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = "<group>"; };
+               A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = matrixoutputcommand.h; sourceTree = "<group>"; };
+               A7E9B74B12D37EC400DA6239 /* memchi2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memchi2.cpp; sourceTree = "<group>"; };
+               A7E9B74C12D37EC400DA6239 /* memchi2.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memchi2.h; sourceTree = "<group>"; };
+               A7E9B74D12D37EC400DA6239 /* memchord.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memchord.cpp; sourceTree = "<group>"; };
+               A7E9B74E12D37EC400DA6239 /* memchord.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = memchord.h; sourceTree = "<group>"; };
+               A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = memeuclidean.cpp; sourceTree = "<group>"; };
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+               A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; 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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+               A7E9B76112D37EC400DA6239 /* nast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nast.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B76212D37EC400DA6239 /* nast.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nast.hpp; sourceTree = SOURCE_ROOT; };
+               A7E9B76312D37EC400DA6239 /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B76412D37EC400DA6239 /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = SOURCE_ROOT; };
+               A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = needlemanoverlap.cpp; sourceTree = SOURCE_ROOT; };
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+               A7E9B76712D37EC400DA6239 /* noalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = noalign.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B76812D37EC400DA6239 /* noalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = noalign.hpp; sourceTree = SOURCE_ROOT; };
+               A7E9B76912D37EC400DA6239 /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = "<group>"; };
+               A7E9B76A12D37EC400DA6239 /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = "<group>"; };
+               A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = "<group>"; };
+               A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = "<group>"; };
+               A7E9B76D12D37EC400DA6239 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = "<group>"; };
+               A7E9B76E12D37EC400DA6239 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = "<group>"; };
+               A7E9B76F12D37EC400DA6239 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = "<group>"; };
+               A7E9B77012D37EC400DA6239 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; };
+               A7E9B77112D37EC400DA6239 /* odum.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = odum.cpp; sourceTree = "<group>"; };
+               A7E9B77212D37EC400DA6239 /* odum.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = odum.h; sourceTree = "<group>"; };
+               A7E9B77312D37EC400DA6239 /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = "<group>"; };
+               A7E9B77412D37EC400DA6239 /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = "<group>"; };
+               A7E9B77512D37EC400DA6239 /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B77612D37EC400DA6239 /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = SOURCE_ROOT; };
+               A7E9B77712D37EC400DA6239 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = "<group>"; };
+               A7E9B77812D37EC400DA6239 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = "<group>"; };
+               A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = "<group>"; };
+               A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = "<group>"; };
+               A7E9B77B12D37EC400DA6239 /* overlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = overlap.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B77C12D37EC400DA6239 /* overlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = overlap.hpp; sourceTree = SOURCE_ROOT; };
+               A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pairwiseseqscommand.cpp; sourceTree = "<group>"; };
+               A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pairwiseseqscommand.h; sourceTree = "<group>"; };
+               A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsefastaqcommand.cpp; sourceTree = "<group>"; };
+               A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsefastaqcommand.h; sourceTree = "<group>"; };
+               A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistscommand.cpp; sourceTree = "<group>"; };
+               A7E9B78212D37EC400DA6239 /* parselistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistscommand.h; sourceTree = "<group>"; };
+               A7E9B78312D37EC400DA6239 /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = "<group>"; };
+               A7E9B78412D37EC400DA6239 /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = "<group>"; };
+               A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.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>"; };
+               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>"; };
+               A7E9B78E12D37EC400DA6239 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = "<group>"; };
+               A7E9B78F12D37EC400DA6239 /* phylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotree.cpp; sourceTree = "<group>"; };
+               A7E9B79012D37EC400DA6239 /* phylotree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotree.h; sourceTree = "<group>"; };
+               A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotypecommand.cpp; sourceTree = "<group>"; };
+               A7E9B79212D37EC400DA6239 /* phylotypecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotypecommand.h; sourceTree = "<group>"; };
+               A7E9B79312D37EC400DA6239 /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = "<group>"; };
+               A7E9B79412D37EC400DA6239 /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = "<group>"; };
+               A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pipelinepdscommand.cpp; sourceTree = "<group>"; };
+               A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pipelinepdscommand.h; sourceTree = "<group>"; };
+               A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = "<group>"; };
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+               A7E9B79912D37EC400DA6239 /* prng.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = prng.cpp; sourceTree = "<group>"; };
+               A7E9B79A12D37EC400DA6239 /* prng.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = prng.h; sourceTree = "<group>"; };
+               A7E9B79B12D37EC400DA6239 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; };
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+               A7E9B79D12D37EC400DA6239 /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = "<group>"; };
+               A7E9B79E12D37EC400DA6239 /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = "<group>"; };
+               A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qualityscores.cpp; sourceTree = "<group>"; };
+               A7E9B7A012D37EC400DA6239 /* qualityscores.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qualityscores.h; sourceTree = "<group>"; };
+               A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = "<group>"; };
+               A7E9B7A212D37EC400DA6239 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = "<group>"; };
+               A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = "<group>"; };
+               A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = "<group>"; };
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+               A7E9B7A612D37EC400DA6239 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = SOURCE_ROOT; };
+               A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B7A812D37EC400DA6239 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = SOURCE_ROOT; };
+               A7E9B7A912D37EC400DA6239 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B7AA12D37EC400DA6239 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = SOURCE_ROOT; };
+               A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = "<group>"; };
+               A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = "<group>"; };
+               A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = SOURCE_ROOT; };
+               A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
+               A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = "<group>"; };
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+               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>"; };
+               A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removelineagecommand.h; sourceTree = "<group>"; };
+               A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotuscommand.cpp; sourceTree = "<group>"; };
+               A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotuscommand.h; sourceTree = "<group>"; };
+               A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = "<group>"; };
+               A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = "<group>"; };
+               A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reportfile.cpp; sourceTree = "<group>"; };
+               A7E9B7CC12D37EC400DA6239 /* reportfile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reportfile.h; sourceTree = "<group>"; };
+               A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reversecommand.cpp; sourceTree = "<group>"; };
+               A7E9B7CE12D37EC400DA6239 /* reversecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reversecommand.h; sourceTree = "<group>"; };
+               A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
+               A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
+               A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = "<group>"; };
+               A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = "<group>"; };
+               A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = "<group>"; };
+               A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = "<group>"; };
+               A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sensspeccommand.cpp; sourceTree = "<group>"; };
+               A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sensspeccommand.h; sourceTree = "<group>"; };
+               A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqerrorcommand.cpp; sourceTree = "<group>"; };
+               A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqerrorcommand.h; sourceTree = "<group>"; };
+               A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = "<group>"; };
+               A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = "<group>"; };
+               A7E9B7DB12D37EC400DA6239 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = "<group>"; };
+               A7E9B7DC12D37EC400DA6239 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = "<group>"; };
+               A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = "<group>"; };
+               A7E9B7DE12D37EC400DA6239 /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = "<group>"; };
+               A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = "<group>"; };
+               A7E9B7E012D37EC400DA6239 /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = "<group>"; };
+               A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = "<group>"; };
+               A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = "<group>"; };
+               A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffinfocommand.cpp; sourceTree = "<group>"; };
+               A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffinfocommand.h; sourceTree = "<group>"; };
+               A7E9B7E512D37EC400DA6239 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = "<group>"; };
+               A7E9B7E612D37EC400DA6239 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = "<group>"; };
+               A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannoneven.cpp; sourceTree = "<group>"; };
+               A7E9B7E812D37EC400DA6239 /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = "<group>"; };
+               A7E9B7E912D37EC400DA6239 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
+               A7E9B7EA12D37EC400DA6239 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
+               A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = "<group>"; };
+               A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = "<group>"; };
+               A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
+               A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = "<group>"; };
+               A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = "<group>"; };
+               A7E9B7F112D37EC400DA6239 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = "<group>"; };
+               A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = "<group>"; };
+               A7E9B7F312D37EC400DA6239 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = "<group>"; };
+               A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = "<group>"; };
+               A7E9B7F512D37EC400DA6239 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = "<group>"; };
+               A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = "<group>"; };
+               A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = "<group>"; };
+               A7E9B7F812D37EC400DA6239 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = "<group>"; };
+               A7E9B7F912D37EC400DA6239 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = "<group>"; };
+               A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = "<group>"; };
+               A7E9B7FB12D37EC400DA6239 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = "<group>"; };
+               A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = "<group>"; };
+               A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = "<group>"; };
+               A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = "<group>"; };
+               A7E9B7FF12D37EC400DA6239 /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = "<group>"; };
+               A7E9B80012D37EC400DA6239 /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = "<group>"; };
+               A7E9B80112D37EC400DA6239 /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = "<group>"; };
+               A7E9B80212D37EC400DA6239 /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = "<group>"; };
+               A7E9B80312D37EC400DA6239 /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = "<group>"; };
+               A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = "<group>"; };
+               A7E9B80512D37EC400DA6239 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = "<group>"; };
+               A7E9B80612D37EC400DA6239 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = "<group>"; };
+               A7E9B80712D37EC400DA6239 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = "<group>"; };
+               A7E9B80812D37EC400DA6239 /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = "<group>"; };
+               A7E9B80912D37EC400DA6239 /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = "<group>"; };
+               A7E9B80A12D37EC400DA6239 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = "<group>"; };
+               A7E9B80B12D37EC400DA6239 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = "<group>"; };
+               A7E9B80C12D37EC400DA6239 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = "<group>"; };
+               A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = "<group>"; };
+               A7E9B80E12D37EC400DA6239 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = "<group>"; };
+               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundfloatvector.cpp; sourceTree = "<group>"; };
+               A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
+               A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = "<group>"; };
+               A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = "<group>"; };
+               A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = "<group>"; };
+               A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = "<group>"; };
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+               A7E9B81912D37EC400DA6239 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = "<group>"; };
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+               A7E9B81C12D37EC400DA6239 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = "<group>"; };
+               A7E9B81D12D37EC400DA6239 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = "<group>"; };
+               A7E9B81E12D37EC400DA6239 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = "<group>"; };
+               A7E9B81F12D37EC400DA6239 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = "<group>"; };
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+               A7E9B82112D37EC400DA6239 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = "<group>"; };
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+               A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B82412D37EC400DA6239 /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = SOURCE_ROOT; };
+               A7E9B82512D37EC400DA6239 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = "<group>"; };
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+               A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shhhercommand.cpp; sourceTree = "<group>"; };
+               A7E9B82812D37EC400DA6239 /* shhhercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shhhercommand.h; sourceTree = "<group>"; };
+               A7E9B82912D37EC400DA6239 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = "<group>"; };
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+               A7E9B82B12D37EC400DA6239 /* simpsoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpsoneven.cpp; sourceTree = "<group>"; };
+               A7E9B82C12D37EC400DA6239 /* simpsoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpsoneven.h; sourceTree = "<group>"; };
+               A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B82E12D37EC400DA6239 /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = "<group>"; };
+               A7E9B82F12D37EC400DA6239 /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = "<group>"; };
+               A7E9B83012D37EC400DA6239 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = SOURCE_ROOT; };
+               A7E9B83112D37EC400DA6239 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = SOURCE_ROOT; };
+               A7E9B83212D37EC400DA6239 /* smithwilson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = smithwilson.cpp; sourceTree = "<group>"; };
+               A7E9B83312D37EC400DA6239 /* smithwilson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = smithwilson.h; sourceTree = "<group>"; };
+               A7E9B83412D37EC400DA6239 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = "<group>"; };
+               A7E9B83512D37EC400DA6239 /* soergel.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = soergel.cpp; sourceTree = "<group>"; };
+               A7E9B83612D37EC400DA6239 /* soergel.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = soergel.h; sourceTree = "<group>"; };
+               A7E9B83712D37EC400DA6239 /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = "<group>"; };
+               A7E9B83812D37EC400DA6239 /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = "<group>"; };
+               A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = "<group>"; };
+               A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = "<group>"; };
+               A7E9B83B12D37EC400DA6239 /* spearman.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = spearman.cpp; sourceTree = "<group>"; };
+               A7E9B83C12D37EC400DA6239 /* spearman.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = spearman.h; sourceTree = "<group>"; };
+               A7E9B83D12D37EC400DA6239 /* speciesprofile.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = speciesprofile.cpp; sourceTree = "<group>"; };
+               A7E9B83E12D37EC400DA6239 /* speciesprofile.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = speciesprofile.h; sourceTree = "<group>"; };
+               A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = "<group>"; };
+               A7E9B84012D37EC400DA6239 /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = "<group>"; };
+               A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitgroupscommand.cpp; sourceTree = "<group>"; };
+               A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitgroupscommand.h; sourceTree = "<group>"; };
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+               A7E9B84512D37EC400DA6239 /* structchi2.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structchi2.cpp; sourceTree = "<group>"; };
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+               A7E9B84712D37EC400DA6239 /* structchord.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structchord.cpp; sourceTree = "<group>"; };
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+               A7E9B84A12D37EC400DA6239 /* structeuclidean.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = structeuclidean.h; sourceTree = "<group>"; };
+               A7E9B84B12D37EC400DA6239 /* structkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structkulczynski.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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+               A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = "<group>"; };
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+               A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = taxonomyequalizer.cpp; sourceTree = "<group>"; };
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+               A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = "<group>"; };
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 /* Begin PBXGroup section */
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                                08FB7795FE84155DC02AAC07 /* Source */,
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                                1AB674ADFE9D54B511CA2CBB /* Products */,
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-                               37519AB40F810FAE00FED5E8 /* venn.cpp */,
+                               A7A61F1A130035C800E05B6B /* LICENSE */,
+                               A70332B512D3A13400761E33 /* makefile */,
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+                               A77B718A173D40E4002163C2 /* calcsparcc.h */,
+                               A77B7189173D40E4002163C2 /* calcsparcc.cpp */,
+                               A7E9BA4F12D398D700DA6239 /* clearcut */,
+                               A7E9B69812D37EC400DA6239 /* cluster.cpp */,
+                               A7E9B69912D37EC400DA6239 /* cluster.hpp */,
+                               A7E9B69A12D37EC400DA6239 /* clusterclassic.cpp */,
+                               A7E9B69B12D37EC400DA6239 /* clusterclassic.h */,
+                               A7E9BA3F12D395F700DA6239 /* calculators */,
+                               A7E9BA4512D3965600DA6239 /* chimera */,
+                               A7E9BA4B12D3966900DA6239 /* classifier */,
+                               A7E9B6A612D37EC400DA6239 /* collect.cpp */,
+                               A7E9B6A712D37EC400DA6239 /* collect.h */,
+                               A7E9B6AA12D37EC400DA6239 /* collectdisplay.h */,
+                               A7E9B6AB12D37EC400DA6239 /* collectorscurvedata.h */,
+                               A7E9BA3812D3956100DA6239 /* commands */,
+                               A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */,
+                               A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */,
+                               A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */,
+                               A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */,
+                               A7DAAFA3133A254E003956EB /* commandparameter.h */,
+                               A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
+                               A7E9BA4212D3960D00DA6239 /* containers */,
+                               A7E9B6B612D37EC400DA6239 /* consensus.h */,
+                               A7E9B6B512D37EC400DA6239 /* consensus.cpp */,
+                               A7AACFBA132FE008003D6C4D /* currentfile.h */,
+                               A7E9B6C912D37EC400DA6239 /* display.h */,
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+                               A7E9B6D212D37EC400DA6239 /* dlibshuff.h */,
+                               A7E9B6D912D37EC400DA6239 /* endiannessmacros.h */,
+                               A7E9B6DA12D37EC400DA6239 /* engine.cpp */,
+                               A7E9B6DB12D37EC400DA6239 /* engine.hpp */,
+                               A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */,
+                               A7E9B6E112D37EC400DA6239 /* fileoutput.h */,
+                               A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */,
+                               A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */,
+                               A7E9B71812D37EC400DA6239 /* hcluster.cpp */,
+                               A7E9B71912D37EC400DA6239 /* hcluster.h */,
+                               A7E9B71C12D37EC400DA6239 /* heatmap.cpp */,
+                               A7E9B71D12D37EC400DA6239 /* heatmap.h */,
+                               A7E9B72012D37EC400DA6239 /* heatmapsim.cpp */,
+                               A7E9B72112D37EC400DA6239 /* heatmapsim.h */,
+                               A7E9B72E12D37EC400DA6239 /* inputdata.h */,
+                               A7E9B72D12D37EC400DA6239 /* inputdata.cpp */,
+                               A7E9B73912D37EC400DA6239 /* libshuff.cpp */,
+                               A7E9B73A12D37EC400DA6239 /* libshuff.h */,
+                               A7FC480C12D788F20055BC5C /* linearalgebra.h */,
+                               A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
+                               A7E9BA5612D39BD800DA6239 /* metastats */,
+                               A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
+                               A7E9B75C12D37EC400DA6239 /* mothur.h */,
+                               A7E9B75D12D37EC400DA6239 /* mothurout.cpp */,
+                               A7E9B75E12D37EC400DA6239 /* mothurout.h */,
+                               A774104714696F320098E6AC /* myseqdist.h */,
+                               A774104614696F320098E6AC /* myseqdist.cpp */,
+                               A7E9B76112D37EC400DA6239 /* nast.cpp */,
+                               A7E9B76212D37EC400DA6239 /* nast.hpp */,
+                               A7E9B76312D37EC400DA6239 /* nastreport.cpp */,
+                               A7E9B76412D37EC400DA6239 /* nastreport.hpp */,
+                               A7E9B76712D37EC400DA6239 /* noalign.cpp */,
+                               A7E9B76812D37EC400DA6239 /* noalign.hpp */,
+                               A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */,
+                               A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */,
+                               A7E9B77012D37EC400DA6239 /* observable.h */,
+                               A7E9B77512D37EC400DA6239 /* optionparser.cpp */,
+                               A7E9B77612D37EC400DA6239 /* optionparser.h */,
+                               A7E9B77B12D37EC400DA6239 /* overlap.cpp */,
+                               A7E9B77C12D37EC400DA6239 /* overlap.hpp */,
+                               A7E9B79B12D37EC400DA6239 /* progress.cpp */,
+                               A7E9B79C12D37EC400DA6239 /* progress.hpp */,
+                               A7548FAF171440ED00B1F05A /* qFinderDMM.h */,
+                               A7548FAE171440EC00B1F05A /* qFinderDMM.cpp */,
+                               A77B7187173D4041002163C2 /* randomnumber.h */,
+                               A77B7186173D4041002163C2 /* randomnumber.cpp */,
+                               A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */,
+                               A7386C191619C9FB00651424 /* randomforest */,
+                               A7E9B7A612D37EC400DA6239 /* rarecalc.h */,
+                               A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */,
+                               A7E9B7A812D37EC400DA6239 /* raredisplay.h */,
+                               A7E9B7A912D37EC400DA6239 /* rarefact.cpp */,
+                               A7E9B7AA12D37EC400DA6239 /* rarefact.h */,
+                               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 */,
+                               A7E9B83112D37EC400DA6239 /* slibshuff.h */,
+                               A7876A28152A018B00A0AE86 /* subsample.h */,
+                               A7876A25152A017C00A0AE86 /* subsample.cpp */,
+                               A7C3DC0E14FE469500FE1924 /* trialswap2.h */,
+                               A7C3DC0D14FE469500FE1924 /* trialSwap2.cpp */,
+                               A7FF19F0140FFDA500AD216D /* trimoligos.h */,
+                               A7FF19F1140FFDA500AD216D /* trimoligos.cpp */,
+                               A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
+                               A7E9B87512D37EC400DA6239 /* validcalculator.h */,
+                               A7E9B87612D37EC400DA6239 /* validparameter.cpp */,
+                               A7E9B87712D37EC400DA6239 /* validparameter.h */,
+                               A7E9B87812D37EC400DA6239 /* venn.cpp */,
+                               A7E9B87912D37EC400DA6239 /* venn.h */,
+                               A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */,
                        );
                        name = Source;
                        sourceTree = "<group>";
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76F6C0486A84900D96B5E /* mothur */,
+                               8DD76FB20486AB0100D96B5E /* mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                };
-               374F2FE81006346600E97C66 /* chimera */ = {
+               A7386C191619C9FB00651424 /* randomforest */ = {
                        isa = PBXGroup;
                        children = (
-                               374F2FD51006320200E97C66 /* chimera.h */,
-                               372095C1103196D70004D347 /* chimera.cpp */,
-                               374F2FE9100634B600E97C66 /* bellerophon.h */,
-                               374F2FEA100634B600E97C66 /* bellerophon.cpp */,
-                               A75B887C104C16860083C454 /* ccode.h */,
-                               A75B887B104C16860083C454 /* ccode.cpp */,
-                               A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */,
-                               A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */,
-                               372A55531017922B00C5194B /* decalc.h */,
-                               372A55541017922B00C5194B /* decalc.cpp */,
-                               374F301110063B6F00E97C66 /* pintail.h */,
-                               374F301210063B6F00E97C66 /* pintail.cpp */,
+                               A7386C1B1619CACB00651424 /* abstractdecisiontree.hpp */,
+                               A7386C241619E52200651424 /* abstractdecisiontree.cpp */,
+                               A7386C1D1619CACB00651424 /* decisiontree.hpp */,
+                               A7386C28161A110700651424 /* decisiontree.cpp */,
+                               A7386C1E1619CACB00651424 /* macros.h */,
+                               A7386C1F1619CACB00651424 /* randomforest.hpp */,
+                               A77E1937161B201E00DB1A2A /* randomforest.cpp */,
+                               A7386C201619CACB00651424 /* rftreenode.hpp */,
+                               A77E193A161B289600DB1A2A /* rftreenode.cpp */,
+                               83F25B0A163B031200ABE73D /* forest.cpp */,
+                               83F25B0B163B031200ABE73D /* forest.h */,
+                               834D9D561656D7C400E7FAB9 /* regularizedrandomforest.cpp */,
+                               834D9D571656D7C400E7FAB9 /* regularizedrandomforest.h */,
+                               834D9D5A1656DEC700E7FAB9 /* regularizeddecisiontree.cpp */,
+                               834D9D5B1656DEC700E7FAB9 /* regularizeddecisiontree.h */,
                        );
-                       name = chimera;
+                       name = randomforest;
                        sourceTree = "<group>";
                };
-               3796441D0FB9B9650081FDB6 /* read */ = {
+               A7D161E7149F7F50000523E8 /* fortran */ = {
                        isa = PBXGroup;
                        children = (
-                               375AA1340F9E433D008EF9B8 /* readcolumn.h */,
-                               375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
-                               37D928130F21331F001D4494 /* readmatrix.hpp */,
-                               375AA1360F9E433D008EF9B8 /* readotu.h */,
-                               375AA1350F9E433D008EF9B8 /* readotu.cpp */,
-                               375AA1380F9E433D008EF9B8 /* readphylip.h */,
-                               375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
-                               37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
-                               37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
+                               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 = read;
+                       name = fortran;
                        sourceTree = "<group>";
                };
-               37D928A60F2133C0001D4494 /* calculators */ = {
+               A7E9BA3812D3956100DA6239 /* commands */ = {
                        isa = PBXGroup;
                        children = (
-                               37D927BE0F21331F001D4494 /* calculator.h */,
-                               37D927BD0F21331F001D4494 /* calculator.cpp */,
-                               3792948D0F2E271100B9034A /* treecalculator.h */,
-                               37D927B90F21331F001D4494 /* ace.h */,
-                               37D927B80F21331F001D4494 /* ace.cpp */,
-                               EB1216860F619B83004A865F /* bergerparker.h */,
-                               EB1216870F619B83004A865F /* bergerparker.cpp */,
-                               373C69950FC1E63600137ACD /* boneh.h */,
-                               373C69940FC1E63600137ACD /* boneh.cpp */,
-                               37D927BC0F21331F001D4494 /* bootstrap.h */,
-                               37D927BB0F21331F001D4494 /* bootstrap.cpp */,
-                               EB1216E30F61ACFB004A865F /* bstick.h */,
-                               EB1216E40F61ACFB004A865F /* bstick.cpp */,
-                               37D927C00F21331F001D4494 /* chao1.h */,
-                               37D927BF0F21331F001D4494 /* chao1.cpp */,
-                               7EC3D4510FA0FFF900338DA5 /* coverage.h */,
-                               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
-                               37C753DF0FB3492400DBD02E /* dist.h */,
-                               37C753F00FB34AE800DBD02E /* eachgapdist.h */,
-                               37C753F40FB34C0300DBD02E /* eachgapignore.h */,
-                               373C69960FC1E63600137ACD /* efron.cpp */,
-                               373C69970FC1E63600137ACD /* efron.h */,
-                               379D3D6B0FF917F40068C1C0 /* filters.h */,
-                               EB9303F70F53517300E8EF26 /* geom.h */,
-                               EB9303F80F53517300E8EF26 /* geom.cpp */,
-                               378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
-                               378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */,
-                               37C753ED0FB34A5700DBD02E /* ignoregaps.h */,
-                               37D927E80F21331F001D4494 /* jackknife.h */,
-                               37D927E70F21331F001D4494 /* jackknife.cpp */,
-                               EB9303E90F534D9400E8EF26 /* logsd.h */,
-                               EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
-                               375873F90F7D64AB0040F377 /* nseqs.h */,
-                               37D927F50F21331F001D4494 /* npshannon.h */,
-                               37D927F40F21331F001D4494 /* npshannon.cpp */,
-                               37C753F10FB34B4700DBD02E /* onegapdist.h */,
-                               37C753F30FB34BBF00DBD02E /* onegapignore.h */,
-                               379294880F2E258500B9034A /* parsimony.h */,
-                               379294890F2E258500B9034A /* parsimony.cpp */,
-                               EB6E68170F5F1C780044E17B /* qstat.h */,
-                               EB6E68180F5F1C780044E17B /* qstat.cpp */,
-                               37D928020F21331F001D4494 /* rarecalc.h */,
-                               37D928010F21331F001D4494 /* rarecalc.cpp */,
-                               37D9281F0F21331F001D4494 /* shannon.h */,
-                               37D9281E0F21331F001D4494 /* shannon.cpp */,
-                               37D928230F21331F001D4494 /* sharedace.h */,
-                               37D928220F21331F001D4494 /* sharedace.cpp */,
-                               37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
-                               37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
-                               7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
-                               375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
-                               375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
-                               37D928250F21331F001D4494 /* sharedchao1.h */,
-                               37D928240F21331F001D4494 /* sharedchao1.cpp */,
-                               37D928290F21331F001D4494 /* sharedjabund.h */,
-                               37D928280F21331F001D4494 /* sharedjabund.cpp */,
-                               378C1B000FB0644D004D63F5 /* sharedjackknife.h */,
-                               378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */,
-                               37D9282B0F21331F001D4494 /* sharedjclass.h */,
-                               37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
-                               37D9282D0F21331F001D4494 /* sharedjest.h */,
-                               37D9282C0F21331F001D4494 /* sharedjest.cpp */,
-                               EB1217210F61C9AC004A865F /* sharedkstest.h */,
-                               EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
-                               375874000F7D64EF0040F377 /* sharedkulczynski.h */,
-                               375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
-                               375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
-                               375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
-                               375874010F7D64EF0040F377 /* sharedlennon.h */,
-                               375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
-                               378C1B020FB0644D004D63F5 /* sharedmarczewski.h */,
-                               378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */,
-                               375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
-                               375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
-                               375874090F7D64FC0040F377 /* sharedochiai.h */,
-                               3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
-                               3758740A0F7D64FC0040F377 /* sharednseqs.h */,
-                               37D928350F21331F001D4494 /* sharedsobs.h */,
-                               37D928340F21331F001D4494 /* sharedsobs.cpp */,
-                               37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
-                               37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
-                               37D928370F21331F001D4494 /* sharedsorabund.h */,
-                               37D928360F21331F001D4494 /* sharedsorabund.cpp */,
-                               37D928390F21331F001D4494 /* sharedsorclass.h */,
-                               37D928380F21331F001D4494 /* sharedsorclass.cpp */,
-                               37D9283B0F21331F001D4494 /* sharedsorest.h */,
-                               37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
-                               37D9283D0F21331F001D4494 /* sharedthetan.h */,
-                               37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
-                               37D9283F0F21331F001D4494 /* sharedthetayc.h */,
-                               37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
-                               EB72FE250FC1F5CA0051AC11 /* shen.h */,
-                               EB72FE240FC1F5CA0051AC11 /* shen.cpp */,
-                               37D928410F21331F001D4494 /* simpson.h */,
-                               37D928400F21331F001D4494 /* simpson.cpp */,
-                               37D928430F21331F001D4494 /* sobs.h */,
-                               373C69980FC1E63600137ACD /* solow.cpp */,
-                               373C69990FC1E63600137ACD /* solow.h */,
-                               374610810F40652400460C57 /* unweighted.h */,
-                               374610820F40652400460C57 /* unweighted.cpp */,
-                               37D9284E0F21331F001D4494 /* uvest.h */,
-                               37D9284D0F21331F001D4494 /* uvest.cpp */,
-                               3746107C0F4064D100460C57 /* weighted.h */,
-                               3746107D0F4064D100460C57 /* weighted.cpp */,
-                               7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
-                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
+                               A7E9B6AE12D37EC400DA6239 /* command.hpp */,
+                               219C1DE11552C508004209F9 /* newcommandtemplate.h */,
+                               219C1DDF1552C4BD004209F9 /* newcommandtemplate.cpp */,
+                               A7E9B65212D37EC300DA6239 /* aligncommand.h */,
+                               A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
+                               A7A61F2B130062E000E05B6B /* amovacommand.h */,
+                               A7A61F2C130062E000E05B6B /* amovacommand.cpp */,
+                               A71CB15F130B04A2001E7287 /* anosimcommand.h */,
+                               A71CB15E130B04A2001E7287 /* anosimcommand.cpp */,
+                               A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
+                               A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
+                               A7E9B67312D37EC400DA6239 /* catchallcommand.h */,
+                               A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
+                               A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */,
+                               A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */,
+                               A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */,
+                               A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */,
+                               A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */,
+                               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 */,
+                               A7386C221619CCE600651424 /* classifysharedcommand.h */,
+                               A7386C211619CCE600651424 /* classifysharedcommand.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 */,
+                               A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */,
+                               A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */,
+                               A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */,
+                               A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */,
+                               A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */,
+                               A7E9B6A912D37EC400DA6239 /* collectcommand.h */,
+                               A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */,
+                               A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */,
+                               A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.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 */,
+                               A77EBD2C1523707F00ED407C /* createdatabasecommand.h */,
+                               A77EBD2E1523709100ED407C /* createdatabasecommand.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 */,
+                               A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
+                               A79EEF8816971D640006DEC1 /* filtersharedcommand.h */,
+                               A79EEF8516971D4A0006DEC1 /* filtersharedcommand.cpp */,
+                               A778FE69134CA6CA00C0BA33 /* getcommandinfocommand.h */,
+                               A778FE6A134CA6CA00C0BA33 /* getcommandinfocommand.cpp */,
+                               219C1DE51559BCF2004209F9 /* getcoremicrobiomecommand.h */,
+                               219C1DE31559BCCD004209F9 /* getcoremicrobiomecommand.cpp */,
+                               A7FE7C3E1330EA1000F7B327 /* getcurrentcommand.h */,
+                               A7FE7C3F1330EA1000F7B327 /* getcurrentcommand.cpp */,
+                               A7128B1A16B7001200723BE4 /* getdistscommand.h */,
+                               A7128B1C16B7002600723BE4 /* getdistscommand.cpp */,
+                               A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
+                               A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
+                               A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */,
+                               A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
+                               A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */,
+                               A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
+                               A7548FAB17142EA500B1F05A /* getmetacommunitycommand.h */,
+                               A7548FAC17142EBC00B1F05A /* getmetacommunitycommand.cpp */,
+                               A70056E8156A93E300924A2D /* getotulabelscommand.h */,
+                               A70056E5156A93D000924A2D /* getotulabelscommand.cpp */,
+                               A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */,
+                               A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
+                               A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */,
+                               A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */,
+                               A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */,
+                               A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */,
+                               A7E9B70112D37EC400DA6239 /* getotuscommand.h */,
+                               A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */,
+                               A7E9B70312D37EC400DA6239 /* getrabundcommand.h */,
+                               A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */,
+                               A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */,
+                               A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */,
+                               A7E9B70712D37EC400DA6239 /* getsabundcommand.h */,
+                               A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */,
+                               A7E9B70912D37EC400DA6239 /* getseqscommand.h */,
+                               A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */,
+                               A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */,
+                               A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */,
+                               A7E9B71B12D37EC400DA6239 /* hclustercommand.h */,
+                               A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */,
+                               A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */,
+                               A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */,
+                               A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */,
+                               A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */,
+                               A7E9B72912D37EC400DA6239 /* helpcommand.h */,
+                               A7E9B72812D37EC400DA6239 /* helpcommand.cpp */,
+                               A75790571301749D00A30DAB /* homovacommand.h */,
+                               A75790581301749D00A30DAB /* homovacommand.cpp */,
+                               A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */,
+                               A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
+                               A7496D2D167B531B00CC7D7C /* kruskalwalliscommand.h */,
+                               A7496D2C167B531B00CC7D7C /* kruskalwalliscommand.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 */,
+                               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */,
+                               A7E6F69C17427CF2006775E2 /* makelookupcommand.h */,
+                               A7E6F69D17427D06006775E2 /* makelookupcommand.cpp */,
+                               A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
+                               A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
+                               A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
+                               A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
+                               A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
+                               A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
+                               A799314816CBD0BC0017E888 /* mergetaxsummarycommand.h */,
+                               A799314A16CBD0CD0017E888 /* mergetaxsummarycommand.cpp */,
+                               A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
+                               A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
+                               A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */,
+                               A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
+                               A7E9B76A12D37EC400DA6239 /* nocommands.h */,
+                               A7E9B76912D37EC400DA6239 /* nocommands.cpp */,
+                               A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.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 */,
+                               A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */,
+                               A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */,
+                               A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */,
+                               A7E9B78212D37EC400DA6239 /* parselistscommand.h */,
+                               A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */,
+                               A7E9B78612D37EC400DA6239 /* parsimonycommand.h */,
+                               A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
+                               A7FC486512D795D60055BC5C /* pcacommand.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 */,
+                               A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */,
+                               A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */,
+                               A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */,
+                               A7E9B79812D37EC400DA6239 /* preclustercommand.h */,
+                               A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */,
+                               A74C06E616A9C097008390A3 /* primerdesigncommand.h */,
+                               A74C06E816A9C0A8008390A3 /* primerdesigncommand.cpp */,
+                               A7E9B7A212D37EC400DA6239 /* quitcommand.h */,
+                               A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */,
+                               A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */,
+                               A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
+                               A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
+                               A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
+                               A7B0231716B8245D006BA09E /* removedistscommand.h */,
+                               A7B0231416B8244B006BA09E /* removedistscommand.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 */,
+                               A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
+                               A7CFA42F1755400500D9ED4D /* renameseqscommand.h */,
+                               A7CFA4301755401800D9ED4D /* renameseqscommand.cpp */,
+                               A7E9B7CE12D37EC400DA6239 /* reversecommand.h */,
+                               A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
+                               A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */,
+                               A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */,
+                               A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */,
+                               A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */,
+                               A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */,
+                               A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */,
+                               A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */,
+                               A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */,
+                               A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */,
+                               A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */,
+                               A7FE7E6B13311EA400F7B327 /* setcurrentcommand.h */,
+                               A7FE7E6C13311EA400F7B327 /* setcurrentcommand.cpp */,
+                               A7E9B7E012D37EC400DA6239 /* setdircommand.h */,
+                               A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */,
+                               A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */,
+                               A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
+                               A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */,
+                               A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
+                               A7C7DAB615DA75760059B0CF /* sffmultiplecommand.h */,
+                               A7C7DAB815DA758B0059B0CF /* sffmultiplecommand.cpp */,
+                               A7E9B7F312D37EC400DA6239 /* sharedcommand.h */,
+                               A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
+                               A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
+                               A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */,
+                               A774101214695AF60098E6AC /* shhhseqscommand.h */,
+                               A774101314695AF60098E6AC /* shhhseqscommand.cpp */,
+                               A7A32DAC14DC43D10001D2E5 /* sortseqscommand.h */,
+                               A7A32DA914DC43B00001D2E5 /* sortseqscommand.cpp */,
+                               A77B7183173D222F002163C2 /* sparcccommand.h */,
+                               A77B7184173D2240002163C2 /* sparcccommand.cpp */,
+                               A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
+                               A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
+                               A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
+                               A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */,
+                               A7E9B85012D37EC400DA6239 /* subsamplecommand.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 */,
+                               A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */,
+                               A7E9B86912D37EC400DA6239 /* trimflowscommand.h */,
+                               A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */,
+                               A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */,
+                               A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */,
+                               A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */,
+                               A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */,
+                               A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */,
+                               A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */,
+                               A7E9B87B12D37EC400DA6239 /* venncommand.h */,
+                               A7E9B87A12D37EC400DA6239 /* venncommand.cpp */,
                        );
-                       name = calculators;
+                       name = commands;
                        sourceTree = "<group>";
                };
-               37D928A90F2133E5001D4494 /* commands */ = {
+               A7E9BA3F12D395F700DA6239 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
-                               37D927CD0F21331F001D4494 /* command.hpp */,
-                               378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
-                               378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
-                               37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
-                               37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
-                               21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
-                               21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
-                               37D927C40F21331F001D4494 /* clustercommand.h */,
-                               37D927C30F21331F001D4494 /* clustercommand.cpp */,
-                               37D927C80F21331F001D4494 /* collectcommand.h */,
-                               37D927C70F21331F001D4494 /* collectcommand.cpp */,
-                               37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
-                               37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
-                               377326640FAF16E0007ABB8B /* consensuscommand.h */,
-                               377326630FAF16E0007ABB8B /* consensuscommand.cpp */,
-                               379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */,
-                               379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */,
-                               37B28F660F27590100808A62 /* deconvolutecommand.h */,
-                               37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
-                               37C753CC0FB3415200DBD02E /* distancecommand.h */,
-                               37C753CD0FB3415200DBD02E /* distancecommand.cpp */,
-                               378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */,
-                               378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */,
-                               A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
-                               A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
-                               A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
-                               A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
-                               A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
-                               A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
-                               370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
-                               370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
-                               3749273D0FD5956B0031C06B /* getrabundcommand.h */,
-                               3749273E0FD5956B0031C06B /* getrabundcommand.cpp */,
-                               3749271B0FD58C840031C06B /* getsabundcommand.h */,
-                               3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
-                               37B73CA41004D89A008C4B41 /* getseqscommand.h */,
-                               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
-                               375873F10F7D64800040F377 /* heatmapcommand.h */,
-                               375873F00F7D64800040F377 /* heatmapcommand.cpp */,
-                               378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
-                               378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */,
-                               37D927E40F21331F001D4494 /* helpcommand.h */,
-                               37D927E30F21331F001D4494 /* helpcommand.cpp */,
-                               375873F40F7D648F0040F377 /* libshuffcommand.h */,
-                               375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
-                               37B73C741004BEFD008C4B41 /* listseqscommand.h */,
-                               37B73C751004BEFD008C4B41 /* listseqscommand.cpp */,
-                               21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
-                               21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
-                               7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
-                               7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
-                               375873F70F7D649C0040F377 /* nocommands.h */,
-                               375873F60F7D649C0040F377 /* nocommands.cpp */,
-                               3792946E0F2E191800B9034A /* parsimonycommand.h */,
-                               3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
-                               37D927FE0F21331F001D4494 /* quitcommand.h */,
-                               37D927FD0F21331F001D4494 /* quitcommand.cpp */,
-                               37D928080F21331F001D4494 /* rarefactcommand.h */,
-                               37D928070F21331F001D4494 /* rarefactcommand.cpp */,
-                               37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
-                               37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
-                               372E12940F263D5A0095CF7E /* readdistcommand.h */,
-                               372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
-                               372E126E0F26365B0095CF7E /* readotucommand.h */,
-                               372E126F0F26365B0095CF7E /* readotucommand.cpp */,
-                               37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
-                               37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
-                               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */,
-                               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
-                               7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
-                               7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
-                               371B30B30FD7EE67000414CA /* screenseqscommand.h */,
-                               371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
-                               3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
-                               3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */,
-                               37D928270F21331F001D4494 /* sharedcommand.h */,
-                               37D928260F21331F001D4494 /* sharedcommand.cpp */,
-                               37D928470F21331F001D4494 /* summarycommand.h */,
-                               37D928460F21331F001D4494 /* summarycommand.cpp */,
-                               37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
-                               37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
-                               37B73CCD1004F5E0008C4B41 /* systemcommand.h */,
-                               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */,
-                               211C38370F961E1F00FEE541 /* treegroupscommand.h */,
-                               211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
-                               7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
-                               7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */,
-                               3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
-                               3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
-                               374610760F40645300460C57 /* unifracweightedcommand.h */,
-                               374610770F40645300460C57 /* unifracweightedcommand.cpp */,
-                               37519A9F0F810D0200FED5E8 /* venncommand.h */,
-                               37519AA00F810D0200FED5E8 /* venncommand.cpp */,
+                               7E78911B135F3E8600E725D2 /* eachgapdistignorens.h */,
+                               A7E9B64F12D37EC300DA6239 /* ace.cpp */,
+                               A7E9B65012D37EC300DA6239 /* ace.h */,
+                               A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */,
+                               A7E9B65F12D37EC300DA6239 /* bergerparker.h */,
+                               A7E9B66612D37EC400DA6239 /* boneh.cpp */,
+                               A7E9B66712D37EC400DA6239 /* boneh.h */,
+                               A7E9B66812D37EC400DA6239 /* bootstrap.cpp */,
+                               A7E9B66912D37EC400DA6239 /* bootstrap.h */,
+                               A7E9B66C12D37EC400DA6239 /* bstick.cpp */,
+                               A7E9B66D12D37EC400DA6239 /* bstick.h */,
+                               A7E9B66E12D37EC400DA6239 /* calculator.cpp */,
+                               A7E9B66F12D37EC400DA6239 /* calculator.h */,
+                               A7E9B67012D37EC400DA6239 /* canberra.cpp */,
+                               A7E9B67112D37EC400DA6239 /* canberra.h */,
+                               A7E9B67612D37EC400DA6239 /* chao1.cpp */,
+                               A7E9B67712D37EC400DA6239 /* chao1.h */,
+                               A7E9B6BB12D37EC400DA6239 /* coverage.cpp */,
+                               A7E9B6BC12D37EC400DA6239 /* coverage.h */,
+                               A7E9B6CA12D37EC400DA6239 /* dist.h */,
+                               A7E9B6C012D37EC400DA6239 /* dayhoff.h */,
+                               A7E9B6D512D37EC400DA6239 /* eachgapdist.h */,
+                               A7E9B6D612D37EC400DA6239 /* eachgapignore.h */,
+                               A7E9B6D712D37EC400DA6239 /* efron.cpp */,
+                               A7E9B6D812D37EC400DA6239 /* efron.h */,
+                               A7E9B6E212D37EC400DA6239 /* filters.h */,
+                               A7E9B6F012D37EC400DA6239 /* geom.cpp */,
+                               A7E9B6F112D37EC400DA6239 /* geom.h */,
+                               A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */,
+                               A7E9B70F12D37EC400DA6239 /* goodscoverage.h */,
+                               A7E9B71212D37EC400DA6239 /* gower.cpp */,
+                               A7E9B71312D37EC400DA6239 /* gower.h */,
+                               A7E9B71612D37EC400DA6239 /* hamming.cpp */,
+                               A7E9B71712D37EC400DA6239 /* hamming.h */,
+                               A7E9B72412D37EC400DA6239 /* heip.cpp */,
+                               A7E9B72512D37EC400DA6239 /* heip.h */,
+                               A7E9B72612D37EC400DA6239 /* hellinger.cpp */,
+                               A7E9B72712D37EC400DA6239 /* hellinger.h */,
+                               A7E9B72A12D37EC400DA6239 /* ignoregaps.h */,
+                               A7E9B72F12D37EC400DA6239 /* invsimpson.cpp */,
+                               A7E9B73012D37EC400DA6239 /* invsimpson.h */,
+                               A7E9B73112D37EC400DA6239 /* jackknife.cpp */,
+                               A7E9B73212D37EC400DA6239 /* jackknife.h */,
+                               A7E9B74112D37EC400DA6239 /* logsd.cpp */,
+                               A7E9B74212D37EC400DA6239 /* logsd.h */,
+                               A7E9B74712D37EC400DA6239 /* manhattan.cpp */,
+                               A7E9B74812D37EC400DA6239 /* manhattan.h */,
+                               A7E9B74B12D37EC400DA6239 /* memchi2.cpp */,
+                               A7E9B74C12D37EC400DA6239 /* memchi2.h */,
+                               A7E9B74D12D37EC400DA6239 /* memchord.cpp */,
+                               A7E9B74E12D37EC400DA6239 /* memchord.h */,
+                               A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */,
+                               A7E9B75012D37EC400DA6239 /* memeuclidean.h */,
+                               A7E9B75112D37EC400DA6239 /* mempearson.cpp */,
+                               A7E9B75212D37EC400DA6239 /* mempearson.h */,
+                               A7E9B76D12D37EC400DA6239 /* npshannon.cpp */,
+                               A7E9B76E12D37EC400DA6239 /* npshannon.h */,
+                               A7E9B76F12D37EC400DA6239 /* nseqs.h */,
+                               A7E9B77112D37EC400DA6239 /* odum.cpp */,
+                               A7E9B77212D37EC400DA6239 /* odum.h */,
+                               A7E9B77312D37EC400DA6239 /* onegapdist.h */,
+                               A7E9B77412D37EC400DA6239 /* onegapignore.h */,
+                               A7E9B78412D37EC400DA6239 /* parsimony.h */,
+                               A7E9B78312D37EC400DA6239 /* parsimony.cpp */,
+                               A7E9B79912D37EC400DA6239 /* prng.cpp */,
+                               A7E9B79A12D37EC400DA6239 /* prng.h */,
+                               A7E9B79D12D37EC400DA6239 /* qstat.cpp */,
+                               A7E9B79E12D37EC400DA6239 /* qstat.h */,
+                               A7E9B7E512D37EC400DA6239 /* shannon.cpp */,
+                               A7E9B7E612D37EC400DA6239 /* shannon.h */,
+                               A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */,
+                               A7E9B7E812D37EC400DA6239 /* shannoneven.h */,
+                               A7E9B7E912D37EC400DA6239 /* sharedace.cpp */,
+                               A7E9B7EA12D37EC400DA6239 /* sharedace.h */,
+                               A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */,
+                               A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */,
+                               A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */,
+                               A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */,
+                               A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */,
+                               A7E9B7F112D37EC400DA6239 /* sharedchao1.h */,
+                               A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */,
+                               A7E9B7F512D37EC400DA6239 /* sharedjabund.h */,
+                               A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */,
+                               A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */,
+                               A7E9B7F812D37EC400DA6239 /* sharedjclass.cpp */,
+                               A7E9B7F912D37EC400DA6239 /* sharedjclass.h */,
+                               A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */,
+                               A7E9B7FB12D37EC400DA6239 /* sharedjest.h */,
+                               A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */,
+                               A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */,
+                               A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */,
+                               A7E9B7FF12D37EC400DA6239 /* sharedkulczynski.h */,
+                               A7E9B80012D37EC400DA6239 /* sharedkulczynskicody.cpp */,
+                               A7E9B80112D37EC400DA6239 /* sharedkulczynskicody.h */,
+                               A7E9B80212D37EC400DA6239 /* sharedlennon.cpp */,
+                               A7E9B80312D37EC400DA6239 /* sharedlennon.h */,
+                               A7E9B80612D37EC400DA6239 /* sharedmarczewski.cpp */,
+                               A7E9B80712D37EC400DA6239 /* sharedmarczewski.h */,
+                               A7E9B80812D37EC400DA6239 /* sharedmorisitahorn.cpp */,
+                               A7E9B80912D37EC400DA6239 /* sharedmorisitahorn.h */,
+                               A7E9B80A12D37EC400DA6239 /* sharednseqs.h */,
+                               A7E9B80B12D37EC400DA6239 /* sharedochiai.cpp */,
+                               A7E9B80C12D37EC400DA6239 /* sharedochiai.h */,
+                               A7E9B81512D37EC400DA6239 /* sharedsobs.cpp */,
+                               A7E9B81612D37EC400DA6239 /* sharedsobs.h */,
+                               A7E9B81712D37EC400DA6239 /* sharedsobscollectsummary.cpp */,
+                               A7E9B81812D37EC400DA6239 /* sharedsobscollectsummary.h */,
+                               A7E9B81912D37EC400DA6239 /* sharedsorabund.cpp */,
+                               A7E9B81A12D37EC400DA6239 /* sharedsorabund.h */,
+                               A7E9B81B12D37EC400DA6239 /* sharedsorclass.cpp */,
+                               A7E9B81C12D37EC400DA6239 /* sharedsorclass.h */,
+                               A7E9B81D12D37EC400DA6239 /* sharedsorest.cpp */,
+                               A7E9B81E12D37EC400DA6239 /* sharedsorest.h */,
+                               A7E9B81F12D37EC400DA6239 /* sharedthetan.cpp */,
+                               A7E9B82012D37EC400DA6239 /* sharedthetan.h */,
+                               A7E9B82112D37EC400DA6239 /* sharedthetayc.cpp */,
+                               A7E9B82212D37EC400DA6239 /* sharedthetayc.h */,
+                               A7E9B82512D37EC400DA6239 /* shen.cpp */,
+                               A7E9B82612D37EC400DA6239 /* shen.h */,
+                               A7E9B82912D37EC400DA6239 /* simpson.cpp */,
+                               A7E9B82A12D37EC400DA6239 /* simpson.h */,
+                               A7E9B82B12D37EC400DA6239 /* simpsoneven.cpp */,
+                               A7E9B82C12D37EC400DA6239 /* simpsoneven.h */,
+                               A7E9B83212D37EC400DA6239 /* smithwilson.cpp */,
+                               A7E9B83312D37EC400DA6239 /* smithwilson.h */,
+                               A7E9B83412D37EC400DA6239 /* sobs.h */,
+                               A7E9B83512D37EC400DA6239 /* soergel.cpp */,
+                               A7E9B83612D37EC400DA6239 /* soergel.h */,
+                               A7E9B83712D37EC400DA6239 /* solow.cpp */,
+                               A7E9B83812D37EC400DA6239 /* solow.h */,
+                               A7E9B83B12D37EC400DA6239 /* spearman.cpp */,
+                               A7E9B83C12D37EC400DA6239 /* spearman.h */,
+                               A7E9B83D12D37EC400DA6239 /* speciesprofile.cpp */,
+                               A7E9B83E12D37EC400DA6239 /* speciesprofile.h */,
+                               A7E9B84512D37EC400DA6239 /* structchi2.cpp */,
+                               A7E9B84612D37EC400DA6239 /* structchi2.h */,
+                               A7E9B84712D37EC400DA6239 /* structchord.cpp */,
+                               A7E9B84812D37EC400DA6239 /* structchord.h */,
+                               A7E9B84912D37EC400DA6239 /* structeuclidean.cpp */,
+                               A7E9B84A12D37EC400DA6239 /* structeuclidean.h */,
+                               A7E9B84B12D37EC400DA6239 /* structkulczynski.cpp */,
+                               A7E9B84C12D37EC400DA6239 /* structkulczynski.h */,
+                               A7E9B84D12D37EC400DA6239 /* structpearson.cpp */,
+                               A7E9B84E12D37EC400DA6239 /* structpearson.h */,
+                               A7E9B86112D37EC400DA6239 /* treecalculator.h */,
+                               A7E9B87112D37EC400DA6239 /* unweighted.h */,
+                               A7E9B87012D37EC400DA6239 /* unweighted.cpp */,
+                               A7E9B87212D37EC400DA6239 /* uvest.cpp */,
+                               A7E9B87312D37EC400DA6239 /* uvest.h */,
+                               A7E9B87D12D37EC400DA6239 /* weighted.h */,
+                               A7E9B87C12D37EC400DA6239 /* weighted.cpp */,
+                               A7E9B87F12D37EC400DA6239 /* whittaker.cpp */,
+                               A7E9B88012D37EC400DA6239 /* whittaker.h */,
                        );
-                       name = commands;
+                       name = calculators;
                        sourceTree = "<group>";
                };
-               37D928AC0F213420001D4494 /* containers */ = {
+               A7E9BA4212D3960D00DA6239 /* containers */ = {
                        isa = PBXGroup;
                        children = (
-                               373C68A10FC1C07D00137ACD /* alignment.hpp */,
-                               373C68A00FC1C07D00137ACD /* alignment.cpp */,
-                               373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
-                               373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
-                               373C69170FC1C8AF00137ACD /* blastdb.hpp */,
-                               373C69160FC1C8AF00137ACD /* blastdb.cpp */,
-                               37D927D40F21331F001D4494 /* database.hpp */,
-                               37D927D30F21331F001D4494 /* database.cpp */,
-                               37D927D50F21331F001D4494 /* datavector.hpp */,
-                               3799A94D0FD6A58C00E33EDE /* distancedb.hpp */,
-                               3799A94C0FD6A58C00E33EDE /* distancedb.cpp */,
-                               37D927DC0F21331F001D4494 /* fastamap.h */,
-                               37D927DB0F21331F001D4494 /* fastamap.cpp */,
-                               375873EA0F7D64520040F377 /* fullmatrix.h */,
-                               375873EB0F7D64520040F377 /* fullmatrix.cpp */,
-                               37D927E20F21331F001D4494 /* groupmap.h */,
-                               37D927E10F21331F001D4494 /* groupmap.cpp */,
-                               37D927EA0F21331F001D4494 /* kmer.hpp */,
-                               37D927E90F21331F001D4494 /* kmer.cpp */,
-                               37D927EC0F21331F001D4494 /* kmerdb.hpp */,
-                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
-                               37D927EE0F21331F001D4494 /* listvector.hpp */,
-                               37D927ED0F21331F001D4494 /* listvector.cpp */,
-                               37D927F80F21331F001D4494 /* ordervector.hpp */,
-                               37D927F70F21331F001D4494 /* ordervector.cpp */,
-                               37D928000F21331F001D4494 /* rabundvector.hpp */,
-                               37D927FF0F21331F001D4494 /* rabundvector.cpp */,
-                               37D9281B0F21331F001D4494 /* sabundvector.hpp */,
-                               37D9281A0F21331F001D4494 /* sabundvector.cpp */,
-                               37D9281D0F21331F001D4494 /* sequence.hpp */,
-                               37D9281C0F21331F001D4494 /* sequence.cpp */,
-                               378C1AFE0FB0644D004D63F5 /* sequencedb.h */,
-                               378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */,
-                               37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
-                               37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
-                               37D9282F0F21331F001D4494 /* sharedordervector.h */,
-                               37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
-                               37D928310F21331F001D4494 /* sharedrabundvector.h */,
-                               37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
-                               37D928330F21331F001D4494 /* sharedsabundvector.h */,
-                               37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
-                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
-                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
-                               373C68F40FC1C6A800137ACD /* suffixdb.hpp */,
-                               373C68F30FC1C6A800137ACD /* suffixdb.cpp */,
-                               373C68F60FC1C6A800137ACD /* suffixnodes.hpp */,
-                               373C68F50FC1C6A800137ACD /* suffixnodes.cpp */,
-                               373C68F80FC1C6A800137ACD /* suffixtree.hpp */,
-                               373C68F70FC1C6A800137ACD /* suffixtree.cpp */,
-                               37AD4DB90F28E2FE00AA2D49 /* tree.h */,
-                               37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
-                               379293C10F2DE73400B9034A /* treemap.h */,
-                               379293C20F2DE73400B9034A /* treemap.cpp */,
-                               37E5F3E10F29FD4200F8D827 /* treenode.h */,
-                               37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
+                               A7E9B65312D37EC300DA6239 /* alignment.cpp */,
+                               A7E9B65412D37EC300DA6239 /* alignment.hpp */,
+                               A7E9B65512D37EC300DA6239 /* alignmentcell.cpp */,
+                               A7E9B65612D37EC300DA6239 /* alignmentcell.hpp */,
+                               A7E9B65712D37EC300DA6239 /* alignmentdb.cpp */,
+                               A7E9B65812D37EC300DA6239 /* alignmentdb.h */,
+                               A7E9B66212D37EC300DA6239 /* blastalign.cpp */,
+                               A7E9B66312D37EC400DA6239 /* blastalign.hpp */,
+                               A7E9B66412D37EC400DA6239 /* blastdb.cpp */,
+                               A7E9B66512D37EC400DA6239 /* blastdb.hpp */,
+                               A74D59A6159A1E3600043046 /* counttable.h */,
+                               A74D59A3159A1E2000043046 /* counttable.cpp */,
+                               A7E9B6BD12D37EC400DA6239 /* database.cpp */,
+                               A7E9B6BE12D37EC400DA6239 /* database.hpp */,
+                               A7E9B6BF12D37EC400DA6239 /* datavector.hpp */,
+                               A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */,
+                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
+                               A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */,
+                               A7E9B6DF12D37EC400DA6239 /* fastamap.h */,
+                               A7E9B6E812D37EC400DA6239 /* flowdata.h */,
+                               A7E9B6E712D37EC400DA6239 /* flowdata.cpp */,
+                               A7E9B6EE12D37EC400DA6239 /* fullmatrix.cpp */,
+                               A7E9B6EF12D37EC400DA6239 /* fullmatrix.h */,
+                               A7E9B71412D37EC400DA6239 /* groupmap.cpp */,
+                               A7E9B71512D37EC400DA6239 /* groupmap.h */,
+                               A7E9B73312D37EC400DA6239 /* kmer.cpp */,
+                               A7E9B73412D37EC400DA6239 /* kmer.hpp */,
+                               A7E9B73512D37EC400DA6239 /* kmerdb.cpp */,
+                               A7E9B73612D37EC400DA6239 /* kmerdb.hpp */,
+                               A7E9B73F12D37EC400DA6239 /* listvector.cpp */,
+                               A7E9B74012D37EC400DA6239 /* listvector.hpp */,
+                               A7E9B75F12D37EC400DA6239 /* nameassignment.cpp */,
+                               A7E9B76012D37EC400DA6239 /* nameassignment.hpp */,
+                               A7E9B77712D37EC400DA6239 /* ordervector.cpp */,
+                               A7E9B77812D37EC400DA6239 /* ordervector.hpp */,
+                               A7E9B79F12D37EC400DA6239 /* qualityscores.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 */,
+                               A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */,
+                               A7E9B7DB12D37EC400DA6239 /* sequence.cpp */,
+                               A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
+                               A741FAD415D168A00067BCC5 /* sequencecountparser.h */,
+                               A741FAD115D1688E0067BCC5 /* sequencecountparser.cpp */,
+                               A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
+                               A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
+                               A7F9F5CD141A5E500032F693 /* sequenceparser.h */,
+                               A7F9F5CE141A5E500032F693 /* sequenceparser.cpp */,
+                               A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */,
+                               A7E9B80512D37EC400DA6239 /* sharedlistvector.h */,
+                               A7E9B80E12D37EC400DA6239 /* sharedordervector.h */,
+                               A7E9B80D12D37EC400DA6239 /* sharedordervector.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 */,
+                               A7E0243F15B4522000A5F046 /* sparsedistancematrix.h */,
+                               A7E0243C15B4520A00A5F046 /* sparsedistancematrix.cpp */,
+                               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 */,
+                               A7E9B86512D37EC400DA6239 /* treemap.h */,
+                               A7E9B86612D37EC400DA6239 /* treenode.cpp */,
+                               A7E9B86712D37EC400DA6239 /* treenode.h */,
                        );
                        name = containers;
                        sourceTree = "<group>";
                };
-               37D928B10F213472001D4494 /* errorcheckor */ = {
+               A7E9BA4512D3965600DA6239 /* chimera */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */,
+                               A7E9B65D12D37EC300DA6239 /* bellerophon.h */,
+                               A7E9B67412D37EC400DA6239 /* ccode.cpp */,
+                               A7E9B67512D37EC400DA6239 /* ccode.h */,
+                               A7E9B67812D37EC400DA6239 /* chimera.cpp */,
+                               A7E9B67912D37EC400DA6239 /* chimera.h */,
+                               A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */,
+                               A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */,
+                               A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */,
+                               A7E9B68512D37EC400DA6239 /* chimerarealigner.h */,
+                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
+                               A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
+                               A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */,
+                               A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
+                               A7E9B74612D37EC400DA6239 /* maligner.h */,
+                               A7E9B74512D37EC400DA6239 /* maligner.cpp */,
+                               A7BF221314587886000AD524 /* myPerseus.h */,
+                               A7BF221214587886000AD524 /* myPerseus.cpp */,
+                               A7E9B79312D37EC400DA6239 /* pintail.cpp */,
+                               A7E9B79412D37EC400DA6239 /* pintail.h */,
+                               A7E9B82E12D37EC400DA6239 /* slayer.cpp */,
+                               A7E9B82F12D37EC400DA6239 /* slayer.h */,
+                       );
+                       name = chimera;
+                       sourceTree = "<group>";
+               };
+               A7E9BA4B12D3966900DA6239 /* classifier */ = {
                        isa = PBXGroup;
                        children = (
-                               37D928500F21331F001D4494 /* validcalculator.h */,
-                               37D9284F0F21331F001D4494 /* validcalculator.cpp */,
-                               37D928540F21331F001D4494 /* validparameter.h */,
-                               37D928530F21331F001D4494 /* validparameter.cpp */,
+                               A721AB67161C570F009860A1 /* alignnode.h */,
+                               A721AB66161C570F009860A1 /* alignnode.cpp */,
+                               A721AB69161C570F009860A1 /* aligntree.h */,
+                               A721AB68161C570F009860A1 /* aligntree.cpp */,
+                               A7E9B65B12D37EC300DA6239 /* bayesian.h */,
+                               A7E9B65A12D37EC300DA6239 /* bayesian.cpp */,
+                               A7E9B68E12D37EC400DA6239 /* classify.cpp */,
+                               A7E9B68F12D37EC400DA6239 /* classify.h */,
+                               A721AB6E161C572A009860A1 /* kmernode.h */,
+                               A721AB6D161C572A009860A1 /* kmernode.cpp */,
+                               A721AB70161C572A009860A1 /* kmertree.h */,
+                               A721AB6F161C572A009860A1 /* kmertree.cpp */,
+                               A7E9B73812D37EC400DA6239 /* knn.h */,
+                               A7E9B73712D37EC400DA6239 /* knn.cpp */,
+                               A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */,
+                               A7E9B78E12D37EC400DA6239 /* phylosummary.h */,
+                               A7E9B78F12D37EC400DA6239 /* phylotree.cpp */,
+                               A7E9B79012D37EC400DA6239 /* phylotree.h */,
+                               A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */,
+                               A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */,
+                               A721AB74161C573B009860A1 /* taxonomynode.h */,
+                               A721AB73161C573B009860A1 /* taxonomynode.cpp */,
                        );
-                       name = errorcheckor;
+                       name = classifier;
                        sourceTree = "<group>";
                };
-               C6859E8C029090F304C91782 /* Documentation */ = {
+               A7E9BA4F12D398D700DA6239 /* clearcut */ = {
                        isa = PBXGroup;
                        children = (
-                               C6859E8B029090EE04C91782 /* Mothur.1 */,
+                               A7E9B69412D37EC400DA6239 /* clearcut.cpp */,
+                               A7E9B69512D37EC400DA6239 /* clearcut.h */,
+                               A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
+                               A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
+                               A7E9B6B312D37EC400DA6239 /* common.h */,
+                               A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */,
+                               A7E9B6D012D37EC400DA6239 /* distclearcut.h */,
+                               A7E9B6D312D37EC400DA6239 /* dmat.cpp */,
+                               A7E9B6D412D37EC400DA6239 /* dmat.h */,
+                               A7E9B6DC12D37EC400DA6239 /* fasta.cpp */,
+                               A7E9B6DD12D37EC400DA6239 /* fasta.h */,
+                               A7E9B6FD12D37EC400DA6239 /* getopt_long.h */,
+                               A7E9B6FC12D37EC400DA6239 /* getopt_long.cpp */,
+                       );
+                       name = clearcut;
+                       sourceTree = "<group>";
+               };
+               A7E9BA5312D39A5E00DA6239 /* read */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */,
+                               A7E9B6EA12D37EC400DA6239 /* formatcolumn.h */,
+                               A7E9B6EB12D37EC400DA6239 /* formatmatrix.h */,
+                               A7E9B6EC12D37EC400DA6239 /* formatphylip.cpp */,
+                               A7E9B6ED12D37EC400DA6239 /* formatphylip.h */,
+                               A7E9B7B012D37EC400DA6239 /* readblast.cpp */,
+                               A7E9B7B112D37EC400DA6239 /* readblast.h */,
+                               A7E9B7B212D37EC400DA6239 /* readcluster.cpp */,
+                               A7E9B7B312D37EC400DA6239 /* readcluster.h */,
+                               A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */,
+                               A7E9B7B512D37EC400DA6239 /* readcolumn.h */,
+                               A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */,
+                               A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */,
+                               A7E9B7BE12D37EC400DA6239 /* readphylip.h */,
+                               A7E9B7BF12D37EC400DA6239 /* readtree.cpp */,
+                               A7E9B7C012D37EC400DA6239 /* readtree.h */,
+                               A713EBAA12DC7613000092AC /* readphylipvector.h */,
+                               A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
+                               A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
+                               A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
+                               A7D755D71535F665009BF21A /* treereader.h */,
+                               A7D755D91535F679009BF21A /* treereader.cpp */,
+                       );
+                       name = read;
+                       sourceTree = "<group>";
+               };
+               A7E9BA5612D39BD800DA6239 /* metastats */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7D161E7149F7F50000523E8 /* fortran */,
+                               A79234D513C74BF6002B08E2 /* mothurfisher.h */,
+                               A79234D613C74BF6002B08E2 /* mothurfisher.cpp */,
+                               A73DDC3613C4BF64006AAE38 /* mothurmetastats.h */,
+                               A73DDC3713C4BF64006AAE38 /* mothurmetastats.cpp */,
+                               A74A9A9D148E881E00AB5E3E /* spline.h */,
+                               A74A9A9E148E881E00AB5E3E /* spline.cpp */,
+                       );
+                       name = metastats;
+                       sourceTree = "<group>";
+               };
+               C6A0FF2B0290797F04C91782 /* Documentation */ = {
+                       isa = PBXGroup;
+                       children = (
+                               C6A0FF2C0290799A04C91782 /* mothur.1 */,
                        );
                        name = Documentation;
                        sourceTree = "<group>";
 /* End PBXGroup section */
 
 /* Begin PBXNativeTarget section */
-               8DD76F620486A84900D96B5E /* mothur */ = {
+               8DD76FA90486AB0100D96B5E /* Mothur */ = {
                        isa = PBXNativeTarget;
-                       buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
+                       buildConfigurationList = 1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */;
                        buildPhases = (
-                               8DD76F640486A84900D96B5E /* Sources */,
-                               8DD76F660486A84900D96B5E /* Frameworks */,
-                               8DD76F690486A84900D96B5E /* CopyFiles */,
+                               8DD76FAB0486AB0100D96B5E /* Sources */,
+                               8DD76FAD0486AB0100D96B5E /* Frameworks */,
+                               8DD76FAF0486AB0100D96B5E /* CopyFiles */,
                        );
                        buildRules = (
+                               A7D162CB149F96CA000523E8 /* PBXBuildRule */,
                        );
                        dependencies = (
                        );
-                       name = mothur;
+                       name = Mothur;
                        productInstallPath = "$(HOME)/bin";
-                       productName = Mothur;
-                       productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
+                       productName = mothur;
+                       productReference = 8DD76FB20486AB0100D96B5E /* mothur */;
                        productType = "com.apple.product-type.tool";
                };
 /* End PBXNativeTarget section */
 /* Begin PBXProject section */
                08FB7793FE84155DC02AAC07 /* Project object */ = {
                        isa = PBXProject;
-                       buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
-                       compatibilityVersion = "Xcode 3.0";
+                       attributes = {
+                               LastUpgradeCheck = 0460;
+                               ORGANIZATIONNAME = "Schloss Lab";
+                       };
+                       buildConfigurationList = 1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */;
+                       compatibilityVersion = "Xcode 3.2";
+                       developmentRegion = English;
                        hasScannedForEncodings = 1;
-                       mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */;
+                       knownRegions = (
+                               English,
+                               Japanese,
+                               French,
+                               German,
+                       );
+                       mainGroup = 08FB7794FE84155DC02AAC07 /* mothur */;
                        projectDirPath = "";
                        projectRoot = "";
                        targets = (
-                               8DD76F620486A84900D96B5E /* mothur */,
+                               8DD76FA90486AB0100D96B5E /* Mothur */,
                        );
                };
 /* End PBXProject section */
 
 /* Begin PBXSourcesBuildPhase section */
-               8DD76F640486A84900D96B5E /* Sources */ = {
+               8DD76FAB0486AB0100D96B5E /* Sources */ = {
                        isa = PBXSourcesBuildPhase;
                        buildActionMask = 2147483647;
                        files = (
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-                               37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */,
-                               37D928570F21331F001D4494 /* bootstrap.cpp in Sources */,
-                               37D928580F21331F001D4494 /* calculator.cpp in Sources */,
-                               37D928590F21331F001D4494 /* chao1.cpp in Sources */,
-                               37D9285A0F21331F001D4494 /* cluster.cpp in Sources */,
-                               37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */,
-                               37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
-                               37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
-                               37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
-                               37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */,
-                               37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
-                               37D928620F21331F001D4494 /* database.cpp in Sources */,
-                               37D928630F21331F001D4494 /* engine.cpp in Sources */,
-                               37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
-                               37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
-                               37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
-                               37D928680F21331F001D4494 /* groupmap.cpp in Sources */,
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-                               37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */,
-                               37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */,
-                               37D9286C0F21331F001D4494 /* kmer.cpp in Sources */,
-                               37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */,
-                               37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
-                               37D9286F0F21331F001D4494 /* mothur.cpp in Sources */,
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-                               37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
-                               37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
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-                               37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */,
-                               37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */,
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-                               37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */,
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-                               37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */,
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-                               37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */,
-                               37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */,
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-                               37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */,
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-                               374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
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-                               374610830F40652400460C57 /* unweighted.cpp in Sources */,
-                               3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
-                               37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
-                               A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
-                               A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
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-                               A7283FF81056CAE100D0CC69 /* chimeracheckrdp.cpp in Sources */,
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+                               A7E9B8F912D37EC400DA6239 /* memchi2.cpp in Sources */,
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+                               A7E9B8FD12D37EC400DA6239 /* mergefilecommand.cpp in Sources */,
+                               A7E9B8FF12D37EC400DA6239 /* metastatscommand.cpp in Sources */,
+                               A7E9B90012D37EC400DA6239 /* mgclustercommand.cpp in Sources */,
+                               A7E9B90112D37EC400DA6239 /* mothur.cpp in Sources */,
+                               A7E9B90212D37EC400DA6239 /* mothurout.cpp in Sources */,
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+                               A7E9B90512D37EC400DA6239 /* nastreport.cpp in Sources */,
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+                               A7E9B90812D37EC400DA6239 /* nocommands.cpp in Sources */,
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+                               A7E9B90A12D37EC400DA6239 /* npshannon.cpp in Sources */,
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+                               A7E9B90C12D37EC400DA6239 /* optionparser.cpp in Sources */,
+                               A7E9B90D12D37EC400DA6239 /* ordervector.cpp in Sources */,
+                               A7E9B90E12D37EC400DA6239 /* otuhierarchycommand.cpp in Sources */,
+                               A7E9B90F12D37EC400DA6239 /* overlap.cpp in Sources */,
+                               A7E9B91012D37EC400DA6239 /* pairwiseseqscommand.cpp in Sources */,
+                               A7E9B91112D37EC400DA6239 /* parsefastaqcommand.cpp in Sources */,
+                               A7E9B91212D37EC400DA6239 /* parselistscommand.cpp in Sources */,
+                               A7E9B91312D37EC400DA6239 /* parsimony.cpp in Sources */,
+                               A7E9B91412D37EC400DA6239 /* parsimonycommand.cpp in Sources */,
+                               A7E9B91512D37EC400DA6239 /* pcoacommand.cpp in Sources */,
+                               A7E9B91712D37EC400DA6239 /* phylodiversitycommand.cpp in Sources */,
+                               A7E9B91812D37EC400DA6239 /* phylosummary.cpp in Sources */,
+                               A7E9B91912D37EC400DA6239 /* phylotree.cpp in Sources */,
+                               A7E9B91A12D37EC400DA6239 /* phylotypecommand.cpp in Sources */,
+                               A7E9B91B12D37EC400DA6239 /* pintail.cpp in Sources */,
+                               A7E9B91C12D37EC400DA6239 /* pipelinepdscommand.cpp in Sources */,
+                               A7E9B91D12D37EC400DA6239 /* preclustercommand.cpp in Sources */,
+                               A7E9B91E12D37EC400DA6239 /* prng.cpp in Sources */,
+                               A7E9B91F12D37EC400DA6239 /* progress.cpp in Sources */,
+                               A7E9B92012D37EC400DA6239 /* qstat.cpp in Sources */,
+                               A7E9B92112D37EC400DA6239 /* qualityscores.cpp in Sources */,
+                               A7E9B92212D37EC400DA6239 /* quitcommand.cpp in Sources */,
+                               A7E9B92312D37EC400DA6239 /* rabundvector.cpp in Sources */,
+                               A7E9B92412D37EC400DA6239 /* rarecalc.cpp in Sources */,
+                               A7E9B92512D37EC400DA6239 /* raredisplay.cpp in Sources */,
+                               A7E9B92612D37EC400DA6239 /* rarefact.cpp in Sources */,
+                               A7E9B92712D37EC400DA6239 /* rarefactcommand.cpp in Sources */,
+                               A7E9B92812D37EC400DA6239 /* rarefactsharedcommand.cpp in Sources */,
+                               A7E9B92912D37EC400DA6239 /* readblast.cpp in Sources */,
+                               A7E9B92A12D37EC400DA6239 /* readcluster.cpp in Sources */,
+                               A7E9B92B12D37EC400DA6239 /* readcolumn.cpp in Sources */,
+                               A7E9B92F12D37EC400DA6239 /* readphylip.cpp in Sources */,
+                               A7E9B93012D37EC400DA6239 /* readtree.cpp in Sources */,
+                               A7E9B93212D37EC400DA6239 /* removegroupscommand.cpp in Sources */,
+                               A7E9B93312D37EC400DA6239 /* removelineagecommand.cpp in Sources */,
+                               A7E9B93412D37EC400DA6239 /* removeotuscommand.cpp in Sources */,
+                               A7E9B93512D37EC400DA6239 /* removeseqscommand.cpp in Sources */,
+                               A7E9B93612D37EC400DA6239 /* reportfile.cpp in Sources */,
+                               A7E9B93712D37EC400DA6239 /* reversecommand.cpp in Sources */,
+                               A7E9B93812D37EC400DA6239 /* sabundvector.cpp in Sources */,
+                               A7E9B93912D37EC400DA6239 /* screenseqscommand.cpp in Sources */,
+                               A7E9B93A12D37EC400DA6239 /* secondarystructurecommand.cpp in Sources */,
+                               A7E9B93B12D37EC400DA6239 /* sensspeccommand.cpp in Sources */,
+                               A7E9B93C12D37EC400DA6239 /* seqerrorcommand.cpp in Sources */,
+                               A7E9B93D12D37EC400DA6239 /* seqsummarycommand.cpp in Sources */,
+                               A7E9B93E12D37EC400DA6239 /* sequence.cpp in Sources */,
+                               A7E9B93F12D37EC400DA6239 /* sequencedb.cpp in Sources */,
+                               A7E9B94012D37EC400DA6239 /* setdircommand.cpp in Sources */,
+                               A7E9B94112D37EC400DA6239 /* setlogfilecommand.cpp in Sources */,
+                               A7E9B94212D37EC400DA6239 /* sffinfocommand.cpp in Sources */,
+                               A7E9B94312D37EC400DA6239 /* shannon.cpp in Sources */,
+                               A7E9B94412D37EC400DA6239 /* shannoneven.cpp in Sources */,
+                               A7E9B94512D37EC400DA6239 /* sharedace.cpp in Sources */,
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                        };
                        name = Debug;
                };
-               1DEB923708733DC60010E9CD /* Release */ = {
+               1DEB928B08733DD80010E9CD /* Release */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               ARCHS = (
-                                       ppc,
-                                       i386,
+                               ARCHS = "$(ARCHS_STANDARD_64_BIT)";
+                               DEPLOYMENT_LOCATION = NO;
+                               GCC_C_LANGUAGE_STANDARD = gnu99;
+                               GCC_GENERATE_DEBUGGING_SYMBOLS = NO;
+                               GCC_MODEL_TUNING = "";
+                               GCC_OPTIMIZATION_LEVEL = s;
+                               GCC_PREPROCESSOR_DEFINITIONS = (
+                                       "VERSION=\"\\\"1.31.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"5/24/2013\\\"\"",
                                );
-                               GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
-                               GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
-                               GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
                                GCC_WARN_MISSING_PARENTHESES = YES;
-                               GCC_WARN_PEDANTIC = YES;
+                               GCC_WARN_MULTIPLE_DEFINITION_TYPES_FOR_SELECTOR = YES;
                                GCC_WARN_UNUSED_FUNCTION = YES;
-                               GCC_WARN_UNUSED_PARAMETER = NO;
+                               GCC_WARN_UNUSED_PARAMETER = YES;
                                GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
+                               INSTALL_PATH = TARGET_BUILD_DIR;
+                               MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
-                                       "-ansi",
-                                       "-pedantic",
-                                       "-wall",
+                                       "-DUSE_READLINE",
+                                       "-DBIT_VERSION",
+                                       "$(OTHER_CFLAGS)",
+                               );
+                               OTHER_LDFLAGS = (
+                                       "-lncurses",
+                                       "-lreadline",
                                );
-                               PREBINDING = NO;
-                               SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
-                               SYMROOT = /Users/johnwestcott/Desktop;
-                               WARNING_CFLAGS = "";
+                               SDKROOT = macosx;
+                               SKIP_INSTALL = NO;
                        };
                        name = Release;
                };
 /* End XCBuildConfiguration section */
 
 /* Begin XCConfigurationList section */
-               1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
+               1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
-                               1DEB923208733DC60010E9CD /* Debug */,
-                               1DEB923308733DC60010E9CD /* Release */,
+                               1DEB928608733DD80010E9CD /* Debug */,
+                               1DEB928708733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
-                       defaultConfigurationName = Release;
+                       defaultConfigurationName = Debug;
                };
-               1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
-                               1DEB923608733DC60010E9CD /* Debug */,
-                               1DEB923708733DC60010E9CD /* Release */,
+                               1DEB928A08733DD80010E9CD /* Debug */,
+                               1DEB928B08733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
-                       defaultConfigurationName = Release;
+                       defaultConfigurationName = Debug;
                };
 /* End XCConfigurationList section */
        };