]> git.donarmstrong.com Git - mothur.git/blob - Mothur.xcodeproj/project.pbxproj
added diffs to trim.seqs
[mothur.git] / Mothur.xcodeproj / project.pbxproj
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98                 A7DA2031113FECD400BF472F /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = "<group>"; };
99                 A7DA2032113FECD400BF472F /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = "<group>"; };
100                 A7DA2033113FECD400BF472F /* coverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = coverage.cpp; sourceTree = "<group>"; };
101                 A7DA2034113FECD400BF472F /* coverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = coverage.h; sourceTree = "<group>"; };
102                 A7DA2035113FECD400BF472F /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = "<group>"; };
103                 A7DA2036113FECD400BF472F /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = "<group>"; };
104                 A7DA2037113FECD400BF472F /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = "<group>"; };
105                 A7DA2038113FECD400BF472F /* decalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = decalc.cpp; sourceTree = "<group>"; };
106                 A7DA2039113FECD400BF472F /* decalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = decalc.h; sourceTree = "<group>"; };
107                 A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
108                 A7DA203B113FECD400BF472F /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
109                 A7DA203C113FECD400BF472F /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = "<group>"; };
110                 A7DA203D113FECD400BF472F /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = "<group>"; };
111                 A7DA203E113FECD400BF472F /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = "<group>"; };
112                 A7DA203F113FECD400BF472F /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = "<group>"; };
113                 A7DA2040113FECD400BF472F /* distancedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancedb.cpp; sourceTree = "<group>"; };
114                 A7DA2041113FECD400BF472F /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = "<group>"; };
115                 A7DA2042113FECD400BF472F /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = "<group>"; };
116                 A7DA2043113FECD400BF472F /* dlibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dlibshuff.h; sourceTree = "<group>"; };
117                 A7DA2044113FECD400BF472F /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = "<group>"; };
118                 A7DA2045113FECD400BF472F /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = "<group>"; };
119                 A7DA2046113FECD400BF472F /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = "<group>"; };
120                 A7DA2047113FECD400BF472F /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = "<group>"; };
121                 A7DA2048113FECD400BF472F /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = "<group>"; };
122                 A7DA2049113FECD400BF472F /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = "<group>"; };
123                 A7DA204A113FECD400BF472F /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = "<group>"; };
124                 A7DA204B113FECD400BF472F /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = "<group>"; };
125                 A7DA204C113FECD400BF472F /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = "<group>"; };
126                 A7DA204D113FECD400BF472F /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = "<group>"; };
127                 A7DA204E113FECD400BF472F /* filters.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filters.h; sourceTree = "<group>"; };
128                 A7DA204F113FECD400BF472F /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = "<group>"; };
129                 A7DA2050113FECD400BF472F /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = "<group>"; };
130                 A7DA2051113FECD400BF472F /* formatcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatcolumn.cpp; sourceTree = "<group>"; };
131                 A7DA2052113FECD400BF472F /* formatcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatcolumn.h; sourceTree = "<group>"; };
132                 A7DA2053113FECD400BF472F /* formatmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatmatrix.h; sourceTree = "<group>"; };
133                 A7DA2054113FECD400BF472F /* formatphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = formatphylip.cpp; sourceTree = "<group>"; };
134                 A7DA2055113FECD400BF472F /* formatphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = formatphylip.h; sourceTree = "<group>"; };
135                 A7DA2056113FECD400BF472F /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = "<group>"; };
136                 A7DA2057113FECD400BF472F /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = "<group>"; };
137                 A7DA2058113FECD400BF472F /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = "<group>"; };
138                 A7DA2059113FECD400BF472F /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = "<group>"; };
139                 A7DA205A113FECD400BF472F /* getgroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupcommand.cpp; sourceTree = "<group>"; };
140                 A7DA205B113FECD400BF472F /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = "<group>"; };
141                 A7DA205C113FECD400BF472F /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = "<group>"; };
142                 A7DA205D113FECD400BF472F /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = "<group>"; };
143                 A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlistcountcommand.cpp; sourceTree = "<group>"; };
144                 A7DA205F113FECD400BF472F /* getlistcountcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlistcountcommand.h; sourceTree = "<group>"; };
145                 A7DA2060113FECD400BF472F /* getoturepcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getoturepcommand.cpp; sourceTree = "<group>"; };
146                 A7DA2061113FECD400BF472F /* getoturepcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getoturepcommand.h; sourceTree = "<group>"; };
147                 A7DA2062113FECD400BF472F /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = "<group>"; };
148                 A7DA2063113FECD400BF472F /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = "<group>"; };
149                 A7DA2064113FECD400BF472F /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = "<group>"; };
150                 A7DA2065113FECD400BF472F /* getsabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsabundcommand.h; sourceTree = "<group>"; };
151                 A7DA2066113FECD400BF472F /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = "<group>"; };
152                 A7DA2067113FECD400BF472F /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = "<group>"; };
153                 A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsharedotucommand.cpp; sourceTree = "<group>"; };
154                 A7DA2069113FECD400BF472F /* getsharedotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getsharedotucommand.h; sourceTree = "<group>"; };
155                 A7DA206A113FECD400BF472F /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = "<group>"; };
156                 A7DA206B113FECD400BF472F /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = "<group>"; };
157                 A7DA206C113FECD400BF472F /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = "<group>"; };
158                 A7DA206D113FECD400BF472F /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = "<group>"; };
159                 A7DA206E113FECD400BF472F /* gotohoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = gotohoverlap.cpp; sourceTree = "<group>"; };
160                 A7DA206F113FECD400BF472F /* gotohoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = gotohoverlap.hpp; sourceTree = "<group>"; };
161                 A7DA2070113FECD400BF472F /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = "<group>"; };
162                 A7DA2071113FECD400BF472F /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = "<group>"; };
163                 A7DA2072113FECD400BF472F /* hcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hcluster.cpp; sourceTree = "<group>"; };
164                 A7DA2073113FECD400BF472F /* hcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hcluster.h; sourceTree = "<group>"; };
165                 A7DA2074113FECD400BF472F /* hclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = hclustercommand.cpp; sourceTree = "<group>"; };
166                 A7DA2075113FECD400BF472F /* hclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = hclustercommand.h; sourceTree = "<group>"; };
167                 A7DA2076113FECD400BF472F /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = "<group>"; };
168                 A7DA2077113FECD400BF472F /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = "<group>"; };
169                 A7DA2078113FECD400BF472F /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = "<group>"; };
170                 A7DA2079113FECD400BF472F /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = "<group>"; };
171                 A7DA207A113FECD400BF472F /* heatmapsim.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsim.cpp; sourceTree = "<group>"; };
172                 A7DA207B113FECD400BF472F /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = "<group>"; };
173                 A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = "<group>"; };
174                 A7DA207D113FECD400BF472F /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = "<group>"; };
175                 A7DA207E113FECD400BF472F /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = "<group>"; };
176                 A7DA207F113FECD400BF472F /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = "<group>"; };
177                 A7DA2080113FECD400BF472F /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = "<group>"; };
178                 A7DA2081113FECD400BF472F /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = "<group>"; };
179                 A7DA2082113FECD400BF472F /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = "<group>"; };
180                 A7DA2083113FECD400BF472F /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = "<group>"; };
181                 A7DA2084113FECD400BF472F /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = "<group>"; };
182                 A7DA2085113FECD400BF472F /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = "<group>"; };
183                 A7DA2086113FECD400BF472F /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = "<group>"; };
184                 A7DA2087113FECD400BF472F /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = "<group>"; };
185                 A7DA2088113FECD400BF472F /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = "<group>"; };
186                 A7DA2089113FECD400BF472F /* knn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = knn.cpp; sourceTree = "<group>"; };
187                 A7DA208A113FECD400BF472F /* knn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = knn.h; sourceTree = "<group>"; };
188                 A7DA208B113FECD400BF472F /* libshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuff.cpp; sourceTree = "<group>"; };
189                 A7DA208C113FECD400BF472F /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = "<group>"; };
190                 A7DA208D113FECD400BF472F /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = "<group>"; };
191                 A7DA208E113FECD400BF472F /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = "<group>"; };
192                 A7DA208F113FECD400BF472F /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = "<group>"; };
193                 A7DA2090113FECD400BF472F /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = "<group>"; };
194                 A7DA2091113FECD400BF472F /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = "<group>"; };
195                 A7DA2092113FECD400BF472F /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = "<group>"; };
196                 A7DA2093113FECD400BF472F /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
197                 A7DA2094113FECD400BF472F /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
198                 A7DA2095113FECD400BF472F /* maligner.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = maligner.cpp; sourceTree = "<group>"; };
199                 A7DA2096113FECD400BF472F /* maligner.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = maligner.h; sourceTree = "<group>"; };
200                 A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = matrixoutputcommand.cpp; sourceTree = "<group>"; };
201                 A7DA2099113FECD400BF472F /* matrixoutputcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = matrixoutputcommand.h; sourceTree = "<group>"; };
202                 A7DA209A113FECD400BF472F /* mergefilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mergefilecommand.cpp; sourceTree = "<group>"; };
203                 A7DA209B113FECD400BF472F /* mergefilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mergefilecommand.h; sourceTree = "<group>"; };
204                 A7DA209C113FECD400BF472F /* mgclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mgclustercommand.cpp; sourceTree = "<group>"; };
205                 A7DA209D113FECD400BF472F /* mgclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mgclustercommand.h; sourceTree = "<group>"; };
206                 A7DA209E113FECD400BF472F /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = "<group>"; };
207                 A7DA209F113FECD400BF472F /* mothur.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothur.h; sourceTree = "<group>"; };
208                 A7DA20A0113FECD400BF472F /* mothurout.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothurout.cpp; sourceTree = "<group>"; };
209                 A7DA20A1113FECD400BF472F /* mothurout.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = mothurout.h; sourceTree = "<group>"; };
210                 A7DA20A2113FECD400BF472F /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = "<group>"; };
211                 A7DA20A3113FECD400BF472F /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = "<group>"; };
212                 A7DA20A4113FECD400BF472F /* nast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nast.cpp; sourceTree = "<group>"; };
213                 A7DA20A5113FECD400BF472F /* nast.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nast.hpp; sourceTree = "<group>"; };
214                 A7DA20A6113FECD400BF472F /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = "<group>"; };
215                 A7DA20A7113FECD400BF472F /* nastreport.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nastreport.hpp; sourceTree = "<group>"; };
216                 A7DA20A8113FECD400BF472F /* needlemanoverlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = needlemanoverlap.cpp; sourceTree = "<group>"; };
217                 A7DA20A9113FECD400BF472F /* needlemanoverlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = needlemanoverlap.hpp; sourceTree = "<group>"; };
218                 A7DA20AA113FECD400BF472F /* noalign.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = noalign.cpp; sourceTree = "<group>"; };
219                 A7DA20AB113FECD400BF472F /* noalign.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = noalign.hpp; sourceTree = "<group>"; };
220                 A7DA20AC113FECD400BF472F /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = "<group>"; };
221                 A7DA20AD113FECD400BF472F /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = "<group>"; };
222                 A7DA20AE113FECD400BF472F /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = "<group>"; };
223                 A7DA20AF113FECD400BF472F /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = "<group>"; };
224                 A7DA20B0113FECD400BF472F /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = "<group>"; };
225                 A7DA20B1113FECD400BF472F /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = "<group>"; };
226                 A7DA20B2113FECD400BF472F /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = "<group>"; };
227                 A7DA20B3113FECD400BF472F /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = "<group>"; };
228                 A7DA20B4113FECD400BF472F /* optionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = optionparser.cpp; sourceTree = "<group>"; };
229                 A7DA20B5113FECD400BF472F /* optionparser.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = optionparser.h; sourceTree = "<group>"; };
230                 A7DA20B6113FECD400BF472F /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = "<group>"; };
231                 A7DA20B7113FECD400BF472F /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = "<group>"; };
232                 A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = otuhierarchycommand.cpp; sourceTree = "<group>"; };
233                 A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = otuhierarchycommand.h; sourceTree = "<group>"; };
234                 A7DA20BA113FECD400BF472F /* overlap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = overlap.cpp; sourceTree = "<group>"; };
235                 A7DA20BB113FECD400BF472F /* overlap.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = overlap.hpp; sourceTree = "<group>"; };
236                 A7DA20BC113FECD400BF472F /* parselistscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistscommand.cpp; sourceTree = "<group>"; };
237                 A7DA20BD113FECD400BF472F /* parselistscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistscommand.h; sourceTree = "<group>"; };
238                 A7DA20BE113FECD400BF472F /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = "<group>"; };
239                 A7DA20BF113FECD400BF472F /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = "<group>"; };
240                 A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = "<group>"; };
241                 A7DA20C1113FECD400BF472F /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
242                 A7DA20C2113FECD400BF472F /* pcacommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pcacommand.cpp; sourceTree = "<group>"; };
243                 A7DA20C3113FECD400BF472F /* pcacommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pcacommand.h; sourceTree = "<group>"; };
244                 A7DA20C4113FECD400BF472F /* phylotree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotree.cpp; sourceTree = "<group>"; };
245                 A7DA20C5113FECD400BF472F /* phylotree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotree.h; sourceTree = "<group>"; };
246                 A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylotypecommand.cpp; sourceTree = "<group>"; };
247                 A7DA20C7113FECD400BF472F /* phylotypecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylotypecommand.h; sourceTree = "<group>"; };
248                 A7DA20C8113FECD400BF472F /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = "<group>"; };
249                 A7DA20C9113FECD400BF472F /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = "<group>"; };
250                 A7DA20CA113FECD400BF472F /* preclustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = preclustercommand.cpp; sourceTree = "<group>"; };
251                 A7DA20CB113FECD400BF472F /* preclustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = preclustercommand.h; sourceTree = "<group>"; };
252                 A7DA20CC113FECD400BF472F /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = "<group>"; };
253                 A7DA20CD113FECD400BF472F /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = "<group>"; };
254                 A7DA20CE113FECD400BF472F /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = "<group>"; };
255                 A7DA20CF113FECD400BF472F /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = "<group>"; };
256                 A7DA20D0113FECD400BF472F /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = "<group>"; };
257                 A7DA20D1113FECD400BF472F /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = "<group>"; };
258                 A7DA20D2113FECD400BF472F /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = "<group>"; };
259                 A7DA20D3113FECD400BF472F /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = "<group>"; };
260                 A7DA20D4113FECD400BF472F /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = "<group>"; };
261                 A7DA20D5113FECD400BF472F /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = "<group>"; };
262                 A7DA20D6113FECD400BF472F /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = "<group>"; };
263                 A7DA20D7113FECD400BF472F /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = "<group>"; };
264                 A7DA20D8113FECD400BF472F /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = "<group>"; };
265                 A7DA20D9113FECD400BF472F /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = "<group>"; };
266                 A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = "<group>"; };
267                 A7DA20DB113FECD400BF472F /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = "<group>"; };
268                 A7DA20DC113FECD400BF472F /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = "<group>"; };
269                 A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
270                 A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = "<group>"; };
271                 A7DA20DF113FECD400BF472F /* readblast.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readblast.cpp; sourceTree = "<group>"; };
272                 A7DA20E0113FECD400BF472F /* readblast.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readblast.h; sourceTree = "<group>"; };
273                 A7DA20E1113FECD400BF472F /* readcluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcluster.cpp; sourceTree = "<group>"; };
274                 A7DA20E2113FECD400BF472F /* readcluster.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcluster.h; sourceTree = "<group>"; };
275                 A7DA20E3113FECD400BF472F /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = "<group>"; };
276                 A7DA20E4113FECD400BF472F /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
277                 A7DA20E5113FECD400BF472F /* readdistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readdistcommand.cpp; sourceTree = "<group>"; };
278                 A7DA20E6113FECD400BF472F /* readdistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readdistcommand.h; sourceTree = "<group>"; };
279                 A7DA20E7113FECD400BF472F /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
280                 A7DA20E8113FECD400BF472F /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = "<group>"; };
281                 A7DA20E9113FECD400BF472F /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = "<group>"; };
282                 A7DA20EA113FECD400BF472F /* readotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotucommand.cpp; sourceTree = "<group>"; };
283                 A7DA20EB113FECD400BF472F /* readotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotucommand.h; sourceTree = "<group>"; };
284                 A7DA20EC113FECD400BF472F /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
285                 A7DA20ED113FECD400BF472F /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
286                 A7DA20EE113FECD400BF472F /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
287                 A7DA20EF113FECD400BF472F /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
288                 A7DA20F0113FECD400BF472F /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
289                 A7DA20F1113FECD400BF472F /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
290                 A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = "<group>"; };
291                 A7DA20F3113FECD400BF472F /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = "<group>"; };
292                 A7DA20F4113FECD400BF472F /* reversecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = reversecommand.cpp; sourceTree = "<group>"; };
293                 A7DA20F5113FECD400BF472F /* reversecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = reversecommand.h; sourceTree = "<group>"; };
294                 A7DA20F6113FECD400BF472F /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
295                 A7DA20F7113FECD400BF472F /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
296                 A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = screenseqscommand.cpp; sourceTree = "<group>"; };
297                 A7DA20F9113FECD400BF472F /* screenseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = screenseqscommand.h; sourceTree = "<group>"; };
298                 A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = secondarystructurecommand.cpp; sourceTree = "<group>"; };
299                 A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = secondarystructurecommand.h; sourceTree = "<group>"; };
300                 A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = "<group>"; };
301                 A7DA20FD113FECD400BF472F /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = "<group>"; };
302                 A7DA20FE113FECD400BF472F /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = "<group>"; };
303                 A7DA20FF113FECD400BF472F /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = "<group>"; };
304                 A7DA2100113FECD400BF472F /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = "<group>"; };
305                 A7DA2101113FECD400BF472F /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = "<group>"; };
306                 A7DA2102113FECD400BF472F /* setdircommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setdircommand.cpp; sourceTree = "<group>"; };
307                 A7DA2103113FECD400BF472F /* setdircommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setdircommand.h; sourceTree = "<group>"; };
308                 A7DA2104113FECD400BF472F /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = "<group>"; };
309                 A7DA2105113FECD400BF472F /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = "<group>"; };
310                 A7DA2106113FECD400BF472F /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
311                 A7DA2107113FECD400BF472F /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
312                 A7DA2108113FECD400BF472F /* sharedanderberg.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderberg.h; sourceTree = "<group>"; };
313                 A7DA2109113FECD400BF472F /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = "<group>"; };
314                 A7DA210A113FECD400BF472F /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = "<group>"; };
315                 A7DA210B113FECD400BF472F /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
316                 A7DA210C113FECD400BF472F /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = "<group>"; };
317                 A7DA210D113FECD400BF472F /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = "<group>"; };
318                 A7DA210E113FECD400BF472F /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = "<group>"; };
319                 A7DA210F113FECD400BF472F /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = "<group>"; };
320                 A7DA2110113FECD400BF472F /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = "<group>"; };
321                 A7DA2111113FECD400BF472F /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = "<group>"; };
322                 A7DA2112113FECD400BF472F /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = "<group>"; };
323                 A7DA2113113FECD400BF472F /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = "<group>"; };
324                 A7DA2114113FECD400BF472F /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = "<group>"; };
325                 A7DA2115113FECD400BF472F /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = "<group>"; };
326                 A7DA2116113FECD400BF472F /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = "<group>"; };
327                 A7DA2117113FECD400BF472F /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = "<group>"; };
328                 A7DA2118113FECD400BF472F /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = "<group>"; };
329                 A7DA2119113FECD400BF472F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = "<group>"; };
330                 A7DA211A113FECD400BF472F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = "<group>"; };
331                 A7DA211B113FECD400BF472F /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = "<group>"; };
332                 A7DA211C113FECD400BF472F /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = "<group>"; };
333                 A7DA211D113FECD400BF472F /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = "<group>"; };
334                 A7DA211E113FECD400BF472F /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = "<group>"; };
335                 A7DA211F113FECD400BF472F /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = "<group>"; };
336                 A7DA2120113FECD400BF472F /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = "<group>"; };
337                 A7DA2121113FECD400BF472F /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = "<group>"; };
338                 A7DA2122113FECD400BF472F /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = "<group>"; };
339                 A7DA2123113FECD400BF472F /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = "<group>"; };
340                 A7DA2124113FECD400BF472F /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = "<group>"; };
341                 A7DA2125113FECD400BF472F /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = "<group>"; };
342                 A7DA2126113FECD400BF472F /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = "<group>"; };
343                 A7DA2127113FECD400BF472F /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = "<group>"; };
344                 A7DA2128113FECD400BF472F /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = "<group>"; };
345                 A7DA2129113FECD400BF472F /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = "<group>"; };
346                 A7DA212A113FECD400BF472F /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = "<group>"; };
347                 A7DA212B113FECD400BF472F /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = "<group>"; };
348                 A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = "<group>"; };
349                 A7DA212D113FECD400BF472F /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = "<group>"; };
350                 A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = "<group>"; };
351                 A7DA212F113FECD400BF472F /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = "<group>"; };
352                 A7DA2130113FECD400BF472F /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = "<group>"; };
353                 A7DA2131113FECD400BF472F /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = "<group>"; };
354                 A7DA2132113FECD400BF472F /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = "<group>"; };
355                 A7DA2133113FECD400BF472F /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = "<group>"; };
356                 A7DA2134113FECD400BF472F /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = "<group>"; };
357                 A7DA2135113FECD400BF472F /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = "<group>"; };
358                 A7DA2136113FECD400BF472F /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = "<group>"; };
359                 A7DA2137113FECD400BF472F /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = "<group>"; };
360                 A7DA2138113FECD400BF472F /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = "<group>"; };
361                 A7DA2139113FECD400BF472F /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = "<group>"; };
362                 A7DA213A113FECD400BF472F /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = "<group>"; };
363                 A7DA213B113FECD400BF472F /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = "<group>"; };
364                 A7DA213C113FECD400BF472F /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = "<group>"; };
365                 A7DA213D113FECD400BF472F /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = "<group>"; };
366                 A7DA213E113FECD400BF472F /* sharedutilities.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedutilities.cpp; sourceTree = "<group>"; };
367                 A7DA213F113FECD400BF472F /* sharedutilities.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedutilities.h; sourceTree = "<group>"; };
368                 A7DA2140113FECD400BF472F /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = "<group>"; };
369                 A7DA2141113FECD400BF472F /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = "<group>"; };
370                 A7DA2142113FECD400BF472F /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = "<group>"; };
371                 A7DA2143113FECD400BF472F /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = "<group>"; };
372                 A7DA2144113FECD400BF472F /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = "<group>"; };
373                 A7DA2145113FECD400BF472F /* slayer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slayer.cpp; sourceTree = "<group>"; };
374                 A7DA2146113FECD400BF472F /* slayer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slayer.h; sourceTree = "<group>"; };
375                 A7DA2147113FECD400BF472F /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = "<group>"; };
376                 A7DA2148113FECD400BF472F /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = "<group>"; };
377                 A7DA2149113FECD400BF472F /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = "<group>"; };
378                 A7DA214A113FECD400BF472F /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = "<group>"; };
379                 A7DA214B113FECD400BF472F /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = "<group>"; };
380                 A7DA214C113FECD400BF472F /* sparsematrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sparsematrix.cpp; sourceTree = "<group>"; };
381                 A7DA214D113FECD400BF472F /* sparsematrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sparsematrix.hpp; sourceTree = "<group>"; };
382                 A7DA214E113FECD400BF472F /* suffixdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixdb.cpp; sourceTree = "<group>"; };
383                 A7DA214F113FECD400BF472F /* suffixdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixdb.hpp; sourceTree = "<group>"; };
384                 A7DA2150113FECD400BF472F /* suffixnodes.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixnodes.cpp; sourceTree = "<group>"; };
385                 A7DA2151113FECD400BF472F /* suffixnodes.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixnodes.hpp; sourceTree = "<group>"; };
386                 A7DA2152113FECD400BF472F /* suffixtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = suffixtree.cpp; sourceTree = "<group>"; };
387                 A7DA2153113FECD400BF472F /* suffixtree.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = suffixtree.hpp; sourceTree = "<group>"; };
388                 A7DA2154113FECD400BF472F /* summarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarycommand.cpp; sourceTree = "<group>"; };
389                 A7DA2155113FECD400BF472F /* summarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarycommand.h; sourceTree = "<group>"; };
390                 A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
391                 A7DA2159113FECD400BF472F /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = "<group>"; };
392                 A7DA215A113FECD400BF472F /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = "<group>"; };
393                 A7DA215B113FECD400BF472F /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = "<group>"; };
394                 A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = taxonomyequalizer.cpp; sourceTree = "<group>"; };
395                 A7DA215D113FECD400BF472F /* taxonomyequalizer.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = taxonomyequalizer.h; sourceTree = "<group>"; };
396                 A7DA215E113FECD400BF472F /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = "<group>"; };
397                 A7DA215F113FECD400BF472F /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = "<group>"; };
398                 A7DA2160113FECD400BF472F /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = "<group>"; };
399                 A7DA2161113FECD400BF472F /* treegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treegroupscommand.cpp; sourceTree = "<group>"; };
400                 A7DA2162113FECD400BF472F /* treegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treegroupscommand.h; sourceTree = "<group>"; };
401                 A7DA2163113FECD400BF472F /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
402                 A7DA2164113FECD400BF472F /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
403                 A7DA2165113FECD400BF472F /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = "<group>"; };
404                 A7DA2166113FECD400BF472F /* treenode.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treenode.h; sourceTree = "<group>"; };
405                 A7DA2167113FECD400BF472F /* trimseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = trimseqscommand.cpp; sourceTree = "<group>"; };
406                 A7DA2168113FECD400BF472F /* trimseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = trimseqscommand.h; sourceTree = "<group>"; };
407                 A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = "<group>"; };
408                 A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = "<group>"; };
409                 A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = "<group>"; };
410                 A7DA216C113FECD400BF472F /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = "<group>"; };
411                 A7DA216D113FECD400BF472F /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = "<group>"; };
412                 A7DA216E113FECD400BF472F /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = "<group>"; };
413                 A7DA216F113FECD400BF472F /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = "<group>"; };
414                 A7DA2170113FECD400BF472F /* uvest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = uvest.h; sourceTree = "<group>"; };
415                 A7DA2171113FECD400BF472F /* validcalculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcalculator.cpp; sourceTree = "<group>"; };
416                 A7DA2172113FECD400BF472F /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = "<group>"; };
417                 A7DA2173113FECD400BF472F /* validparameter.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validparameter.cpp; sourceTree = "<group>"; };
418                 A7DA2174113FECD400BF472F /* validparameter.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validparameter.h; sourceTree = "<group>"; };
419                 A7DA2175113FECD400BF472F /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = "<group>"; };
420                 A7DA2176113FECD400BF472F /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = "<group>"; };
421                 A7DA2177113FECD400BF472F /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = "<group>"; };
422                 A7DA2178113FECD400BF472F /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = "<group>"; };
423                 A7DA2179113FECD400BF472F /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = "<group>"; };
424                 A7DA217A113FECD400BF472F /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
425                 A7DA217B113FECD400BF472F /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
426                 A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
427                 A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsesffcommand.cpp; sourceTree = "<group>"; };
428                 A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = "<group>"; };
429 /* End PBXFileReference section */
430
431 /* Begin PBXGroup section */
432                 08FB7794FE84155DC02AAC07 /* mothur */ = {
433                         isa = PBXGroup;
434                         children = (
435                                 A7639F8D1175DF35008F5578 /* makefile */,
436                                 A7DA1FF0113FECD400BF472F /* alignment.cpp */,
437                                 A7DA1FF1113FECD400BF472F /* alignment.hpp */,
438                                 A7DA1FF6113FECD400BF472F /* averagelinkage.cpp */,
439                                 A7DA2000113FECD400BF472F /* blastalign.hpp */,
440                                 A7DA1FFF113FECD400BF472F /* blastalign.cpp */,
441                                 A7DA201F113FECD400BF472F /* cluster.cpp */,
442                                 A7DA2020113FECD400BF472F /* cluster.hpp */,
443                                 A7CB593B11402EF90010EB83 /* calculators */,
444                                 A7CB594A11402FB40010EB83 /* chimeras */,
445                                 A7CB594511402F6E0010EB83 /* classifers */,
446                                 A7CB593E11402F110010EB83 /* commands */,
447                                 A7CB594211402F430010EB83 /* containers */,
448                                 A7DA2023113FECD400BF472F /* collect.cpp */,
449                                 A7DA2024113FECD400BF472F /* collect.h */,
450                                 A7DA2027113FECD400BF472F /* collectdisplay.h */,
451                                 A7DA2028113FECD400BF472F /* collectorscurvedata.h */,
452                                 A7DA202C113FECD400BF472F /* commandfactory.cpp */,
453                                 A7DA202D113FECD400BF472F /* commandfactory.hpp */,
454                                 A7DA202E113FECD400BF472F /* commandoptionparser.cpp */,
455                                 A7DA202F113FECD400BF472F /* commandoptionparser.hpp */,
456                                 A7DA2030113FECD400BF472F /* completelinkage.cpp */,
457                                 A7DA203C113FECD400BF472F /* display.h */,
458                                 A7DA2042113FECD400BF472F /* dlibshuff.cpp */,
459                                 A7DA2043113FECD400BF472F /* dlibshuff.h */,
460                                 A7DA2048113FECD400BF472F /* engine.cpp */,
461                                 A7DA2049113FECD400BF472F /* engine.hpp */,
462                                 A7DA204C113FECD400BF472F /* fileoutput.cpp */,
463                                 A7DA204D113FECD400BF472F /* fileoutput.h */,
464                                 A7DA206A113FECD400BF472F /* globaldata.cpp */,
465                                 A7DA206B113FECD400BF472F /* globaldata.hpp */,
466                                 A7DA206E113FECD400BF472F /* gotohoverlap.cpp */,
467                                 A7DA206F113FECD400BF472F /* gotohoverlap.hpp */,
468                                 A7DA2072113FECD400BF472F /* hcluster.cpp */,
469                                 A7DA2073113FECD400BF472F /* hcluster.h */,
470                                 A7DA2076113FECD400BF472F /* heatmap.cpp */,
471                                 A7DA2077113FECD400BF472F /* heatmap.h */,
472                                 A7DA207A113FECD400BF472F /* heatmapsim.cpp */,
473                                 A7DA207B113FECD400BF472F /* heatmapsim.h */,
474                                 A7DA2081113FECD400BF472F /* inputdata.cpp */,
475                                 A7DA2082113FECD400BF472F /* inputdata.h */,
476                                 A7DA208B113FECD400BF472F /* libshuff.cpp */,
477                                 A7DA208C113FECD400BF472F /* libshuff.h */,
478                                 A7DA209E113FECD400BF472F /* mothur.cpp */,
479                                 A7DA209F113FECD400BF472F /* mothur.h */,
480                                 A7DA20A0113FECD400BF472F /* mothurout.cpp */,
481                                 A7DA20A1113FECD400BF472F /* mothurout.h */,
482                                 A7DA20A4113FECD400BF472F /* nast.cpp */,
483                                 A7DA20A5113FECD400BF472F /* nast.hpp */,
484                                 A7DA20A6113FECD400BF472F /* nastreport.cpp */,
485                                 A7DA20A7113FECD400BF472F /* nastreport.hpp */,
486                                 A7DA20A8113FECD400BF472F /* needlemanoverlap.cpp */,
487                                 A7DA20A9113FECD400BF472F /* needlemanoverlap.hpp */,
488                                 A7DA20AA113FECD400BF472F /* noalign.cpp */,
489                                 A7DA20AB113FECD400BF472F /* noalign.hpp */,
490                                 A7DA20B1113FECD400BF472F /* observable.h */,
491                                 A7DA20B4113FECD400BF472F /* optionparser.cpp */,
492                                 A7DA20B5113FECD400BF472F /* optionparser.h */,
493                                 A7DA20BA113FECD400BF472F /* overlap.cpp */,
494                                 A7DA20BB113FECD400BF472F /* overlap.hpp */,
495                                 A7DA20CC113FECD400BF472F /* progress.cpp */,
496                                 A7DA20CD113FECD400BF472F /* progress.hpp */,
497                                 A7DA20D4113FECD400BF472F /* rarecalc.cpp */,
498                                 A7DA20D5113FECD400BF472F /* rarecalc.h */,
499                                 A7DA20D6113FECD400BF472F /* raredisplay.cpp */,
500                                 A7DA20D7113FECD400BF472F /* raredisplay.h */,
501                                 A7DA20D8113FECD400BF472F /* rarefact.cpp */,
502                                 A7DA20D9113FECD400BF472F /* rarefact.h */,
503                                 A7DA20DC113FECD400BF472F /* rarefactioncurvedata.h */,
504                                 A7CB5953114033220010EB83 /* read */,
505                                 A7DA213E113FECD400BF472F /* sharedutilities.cpp */,
506                                 A7DA213F113FECD400BF472F /* sharedutilities.h */,
507                                 A7DA2144113FECD400BF472F /* singlelinkage.cpp */,
508                                 A7DA2147113FECD400BF472F /* slibshuff.cpp */,
509                                 A7DA2148113FECD400BF472F /* slibshuff.h */,
510                                 A7DA2171113FECD400BF472F /* validcalculator.cpp */,
511                                 A7DA2172113FECD400BF472F /* validcalculator.h */,
512                                 A7DA2173113FECD400BF472F /* validparameter.cpp */,
513                                 A7DA2174113FECD400BF472F /* validparameter.h */,
514                                 A7DA2175113FECD400BF472F /* venn.cpp */,
515                                 A7DA2176113FECD400BF472F /* venn.h */,
516                         );
517                         name = mothur;
518                         sourceTree = "<group>";
519                 };
520                 A7CB593B11402EF90010EB83 /* calculators */ = {
521                         isa = PBXGroup;
522                         children = (
523                                 A7DA200B113FECD400BF472F /* calculator.cpp */,
524                                 A7DA200C113FECD400BF472F /* calculator.h */,
525                                 A7DA1FED113FECD400BF472F /* ace.h */,
526                                 A7DA1FEC113FECD400BF472F /* ace.cpp */,
527                                 A7DA1FFB113FECD400BF472F /* bergerparker.cpp */,
528                                 A7DA1FFC113FECD400BF472F /* bergerparker.h */,
529                                 A7DA2003113FECD400BF472F /* boneh.cpp */,
530                                 A7DA2004113FECD400BF472F /* boneh.h */,
531                                 A7DA2005113FECD400BF472F /* bootstrap.cpp */,
532                                 A7DA2006113FECD400BF472F /* bootstrap.h */,
533                                 A7DA2009113FECD400BF472F /* bstick.cpp */,
534                                 A7DA200A113FECD400BF472F /* bstick.h */,
535                                 A7DA200F113FECD400BF472F /* chao1.cpp */,
536                                 A7DA2010113FECD400BF472F /* chao1.h */,
537                                 A7DA2033113FECD400BF472F /* coverage.cpp */,
538                                 A7DA2034113FECD400BF472F /* coverage.h */,
539                                 A7DA203D113FECD400BF472F /* dist.h */,
540                                 A7DA2044113FECD400BF472F /* eachgapdist.h */,
541                                 A7DA2045113FECD400BF472F /* eachgapignore.h */,
542                                 A7DA2046113FECD400BF472F /* efron.cpp */,
543                                 A7DA2047113FECD400BF472F /* efron.h */,
544                                 A7DA204E113FECD400BF472F /* filters.h */,
545                                 A7DA2058113FECD400BF472F /* geom.cpp */,
546                                 A7DA2059113FECD400BF472F /* geom.h */,
547                                 A7DA206C113FECD400BF472F /* goodscoverage.cpp */,
548                                 A7DA206D113FECD400BF472F /* goodscoverage.h */,
549                                 A7DA2080113FECD400BF472F /* ignoregaps.h */,
550                                 A7DA2083113FECD400BF472F /* jackknife.cpp */,
551                                 A7DA2084113FECD400BF472F /* jackknife.h */,
552                                 A7DA2093113FECD400BF472F /* logsd.cpp */,
553                                 A7DA2094113FECD400BF472F /* logsd.h */,
554                                 A7DA20AE113FECD400BF472F /* npshannon.cpp */,
555                                 A7DA20AF113FECD400BF472F /* npshannon.h */,
556                                 A7DA20B0113FECD400BF472F /* nseqs.h */,
557                                 A7DA20B2113FECD400BF472F /* onegapdist.h */,
558                                 A7DA20B3113FECD400BF472F /* onegapignore.h */,
559                                 A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */,
560                                 A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */,
561                                 A7DA20BE113FECD400BF472F /* parsimony.cpp */,
562                                 A7DA20BF113FECD400BF472F /* parsimony.h */,
563                                 A7DA20CE113FECD400BF472F /* qstat.cpp */,
564                                 A7DA20CF113FECD400BF472F /* qstat.h */,
565                                 A7DA2104113FECD400BF472F /* shannon.cpp */,
566                                 A7DA2105113FECD400BF472F /* shannon.h */,
567                                 A7DA2106113FECD400BF472F /* sharedace.cpp */,
568                                 A7DA2107113FECD400BF472F /* sharedace.h */,
569                                 A7DA2108113FECD400BF472F /* sharedanderberg.h */,
570                                 A7DA2109113FECD400BF472F /* sharedanderbergs.cpp */,
571                                 A7DA210A113FECD400BF472F /* sharedanderbergs.h */,
572                                 A7DA210B113FECD400BF472F /* sharedbraycurtis.cpp */,
573                                 A7DA210C113FECD400BF472F /* sharedbraycurtis.h */,
574                                 A7DA210D113FECD400BF472F /* sharedchao1.cpp */,
575                                 A7DA210E113FECD400BF472F /* sharedchao1.h */,
576                                 A7DA2111113FECD400BF472F /* sharedjabund.cpp */,
577                                 A7DA2112113FECD400BF472F /* sharedjabund.h */,
578                                 A7DA2113113FECD400BF472F /* sharedjackknife.cpp */,
579                                 A7DA2114113FECD400BF472F /* sharedjackknife.h */,
580                                 A7DA2115113FECD400BF472F /* sharedjclass.cpp */,
581                                 A7DA2116113FECD400BF472F /* sharedjclass.h */,
582                                 A7DA2117113FECD400BF472F /* sharedjest.cpp */,
583                                 A7DA2118113FECD400BF472F /* sharedjest.h */,
584                                 A7DA2119113FECD400BF472F /* sharedkstest.cpp */,
585                                 A7DA211A113FECD400BF472F /* sharedkstest.h */,
586                                 A7DA211B113FECD400BF472F /* sharedkulczynski.cpp */,
587                                 A7DA211C113FECD400BF472F /* sharedkulczynski.h */,
588                                 A7DA211D113FECD400BF472F /* sharedkulczynskicody.cpp */,
589                                 A7DA211E113FECD400BF472F /* sharedkulczynskicody.h */,
590                                 A7DA211F113FECD400BF472F /* sharedlennon.cpp */,
591                                 A7DA2120113FECD400BF472F /* sharedlennon.h */,
592                                 A7DA2123113FECD400BF472F /* sharedmarczewski.cpp */,
593                                 A7DA2124113FECD400BF472F /* sharedmarczewski.h */,
594                                 A7DA2125113FECD400BF472F /* sharedmorisitahorn.cpp */,
595                                 A7DA2126113FECD400BF472F /* sharedmorisitahorn.h */,
596                                 A7DA2127113FECD400BF472F /* sharednseqs.h */,
597                                 A7DA2128113FECD400BF472F /* sharedochiai.cpp */,
598                                 A7DA2129113FECD400BF472F /* sharedochiai.h */,
599                                 A7DA2130113FECD400BF472F /* sharedsobs.cpp */,
600                                 A7DA2131113FECD400BF472F /* sharedsobs.h */,
601                                 A7DA2132113FECD400BF472F /* sharedsobscollectsummary.cpp */,
602                                 A7DA2133113FECD400BF472F /* sharedsobscollectsummary.h */,
603                                 A7DA2134113FECD400BF472F /* sharedsorabund.cpp */,
604                                 A7DA2135113FECD400BF472F /* sharedsorabund.h */,
605                                 A7DA2136113FECD400BF472F /* sharedsorclass.cpp */,
606                                 A7DA2137113FECD400BF472F /* sharedsorclass.h */,
607                                 A7DA2138113FECD400BF472F /* sharedsorest.cpp */,
608                                 A7DA2139113FECD400BF472F /* sharedsorest.h */,
609                                 A7DA213A113FECD400BF472F /* sharedthetan.cpp */,
610                                 A7DA213B113FECD400BF472F /* sharedthetan.h */,
611                                 A7DA213C113FECD400BF472F /* sharedthetayc.cpp */,
612                                 A7DA213D113FECD400BF472F /* sharedthetayc.h */,
613                                 A7DA2140113FECD400BF472F /* shen.cpp */,
614                                 A7DA2141113FECD400BF472F /* shen.h */,
615                                 A7DA2142113FECD400BF472F /* simpson.cpp */,
616                                 A7DA2143113FECD400BF472F /* simpson.h */,
617                                 A7DA2149113FECD400BF472F /* sobs.h */,
618                                 A7DA214A113FECD400BF472F /* solow.cpp */,
619                                 A7DA214B113FECD400BF472F /* solow.h */,
620                                 A7DA2160113FECD400BF472F /* treecalculator.h */,
621                                 A7DA216D113FECD400BF472F /* unweighted.cpp */,
622                                 A7DA216E113FECD400BF472F /* unweighted.h */,
623                                 A7DA216F113FECD400BF472F /* uvest.cpp */,
624                                 A7DA2170113FECD400BF472F /* uvest.h */,
625                                 A7DA2179113FECD400BF472F /* weighted.cpp */,
626                                 A7DA217A113FECD400BF472F /* weighted.h */,
627                                 A7DA217B113FECD400BF472F /* whittaker.cpp */,
628                                 A7DA217C113FECD400BF472F /* whittaker.h */,
629                         );
630                         name = calculators;
631                         sourceTree = "<group>";
632                 };
633                 A7CB593E11402F110010EB83 /* commands */ = {
634                         isa = PBXGroup;
635                         children = (
636                                 A7DA202B113FECD400BF472F /* command.hpp */,
637                                 A7DA1FEF113FECD400BF472F /* aligncommand.h */,
638                                 A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,
639                                 A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
640                                 A7DA1FFE113FECD400BF472F /* binsequencecommand.h */,
641                                 A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
642                                 A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
643                                 A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
644                                 A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
645                                 A7825502116519F70002E2DD /* chimerabellerophoncommand.h */,
646                                 A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */,
647                                 A747E79B1163442A00FB9042 /* chimeracheckcommand.h */,
648                                 A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */,
649                                 A78434881162224F00100BE0 /* chimeraccodecommand.h */,
650                                 A78434891162224F00100BE0 /* chimeraccodecommand.cpp */,
651                                 A78254461164D7790002E2DD /* chimerapintailcommand.h */,
652                                 A78254471164D7790002E2DD /* chimerapintailcommand.cpp */,
653                                 A747E81C116365E000FB9042 /* chimeraslayercommand.h */,
654                                 A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */,
655                                 A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
656                                 A7DA201E113FECD400BF472F /* classifyseqscommand.h */,
657                                 A7DA2021113FECD400BF472F /* clustercommand.cpp */,
658                                 A7DA2022113FECD400BF472F /* clustercommand.h */,
659                                 A7DA2025113FECD400BF472F /* collectcommand.cpp */,
660                                 A7DA2026113FECD400BF472F /* collectcommand.h */,
661                                 A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
662                                 A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
663                                 A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
664                                 A7DA2032113FECD400BF472F /* consensuscommand.h */,
665                                 A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
666                                 A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
667                                 A7DA203E113FECD400BF472F /* distancecommand.cpp */,
668                                 A7DA203F113FECD400BF472F /* distancecommand.h */,
669                                 A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
670                                 A7DA2050113FECD400BF472F /* filterseqscommand.h */,
671                                 A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
672                                 A7DA205B113FECD400BF472F /* getgroupcommand.h */,
673                                 A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
674                                 A7DA205D113FECD400BF472F /* getlabelcommand.h */,
675                                 A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
676                                 A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
677                                 A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
678                                 A7DA2061113FECD400BF472F /* getoturepcommand.h */,
679                                 A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
680                                 A7DA2063113FECD400BF472F /* getrabundcommand.h */,
681                                 A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
682                                 A7DA2065113FECD400BF472F /* getsabundcommand.h */,
683                                 A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
684                                 A7DA2067113FECD400BF472F /* getseqscommand.h */,
685                                 A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
686                                 A7DA2069113FECD400BF472F /* getsharedotucommand.h */,
687                                 A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
688                                 A7DA2075113FECD400BF472F /* hclustercommand.h */,
689                                 A7DA2078113FECD400BF472F /* heatmapcommand.cpp */,
690                                 A7DA2079113FECD400BF472F /* heatmapcommand.h */,
691                                 A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */,
692                                 A7DA207D113FECD400BF472F /* heatmapsimcommand.h */,
693                                 A7DA207E113FECD400BF472F /* helpcommand.cpp */,
694                                 A7DA207F113FECD400BF472F /* helpcommand.h */,
695                                 A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
696                                 A7DA208E113FECD400BF472F /* libshuffcommand.h */,
697                                 A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
698                                 A7DA2090113FECD400BF472F /* listseqscommand.h */,
699                                 A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
700                                 A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
701                                 A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
702                                 A7DA209B113FECD400BF472F /* mergefilecommand.h */,
703                                 A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
704                                 A7DA209D113FECD400BF472F /* mgclustercommand.h */,
705                                 A7DA20AC113FECD400BF472F /* nocommands.cpp */,
706                                 A7DA20AD113FECD400BF472F /* nocommands.h */,
707                                 A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
708                                 A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
709                                 A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
710                                 A7DA20BD113FECD400BF472F /* parselistscommand.h */,
711                                 A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
712                                 A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
713                                 A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
714                                 A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
715                                 A7DA20C3113FECD400BF472F /* pcacommand.h */,
716                                 A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
717                                 A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */,
718                                 A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */,
719                                 A7DA20C7113FECD400BF472F /* phylotypecommand.h */,
720                                 A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
721                                 A7DA20CB113FECD400BF472F /* preclustercommand.h */,
722                                 A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
723                                 A7DA20D1113FECD400BF472F /* quitcommand.h */,
724                                 A7DA20D0113FECD400BF472F /* quitcommand.cpp */,
725                                 A7DA20DB113FECD400BF472F /* rarefactcommand.h */,
726                                 A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */,
727                                 A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */,
728                                 A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */,
729                                 A7DA20E6113FECD400BF472F /* readdistcommand.h */,
730                                 A7DA20E5113FECD400BF472F /* readdistcommand.cpp */,
731                                 A7DA20EB113FECD400BF472F /* readotucommand.h */,
732                                 A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
733                                 A7DA20F1113FECD400BF472F /* readtreecommand.h */,
734                                 A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
735                                 A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
736                                 A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
737                                 A7DA20F5113FECD400BF472F /* reversecommand.h */,
738                                 A7DA20F4113FECD400BF472F /* reversecommand.cpp */,
739                                 A7DA20F9113FECD400BF472F /* screenseqscommand.h */,
740                                 A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
741                                 A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */,
742                                 A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
743                                 A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
744                                 A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
745                                 A7DA2103113FECD400BF472F /* setdircommand.h */,
746                                 A7DA2102113FECD400BF472F /* setdircommand.cpp */,
747                                 A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
748                                 A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
749                                 A7DA2110113FECD400BF472F /* sharedcommand.h */,
750                                 A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
751                                 A7DA2155113FECD400BF472F /* summarycommand.h */,
752                                 A7DA2154113FECD400BF472F /* summarycommand.cpp */,
753                                 A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
754                                 A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */,
755                                 A7DA215B113FECD400BF472F /* systemcommand.h */,
756                                 A7DA215A113FECD400BF472F /* systemcommand.cpp */,
757                                 A7DA2162113FECD400BF472F /* treegroupscommand.h */,
758                                 A7DA2161113FECD400BF472F /* treegroupscommand.cpp */,
759                                 A7DA2168113FECD400BF472F /* trimseqscommand.h */,
760                                 A7DA2167113FECD400BF472F /* trimseqscommand.cpp */,
761                                 A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */,
762                                 A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */,
763                                 A7DA216C113FECD400BF472F /* unifracweightedcommand.h */,
764                                 A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */,
765                                 A7DA2178113FECD400BF472F /* venncommand.h */,
766                                 A7DA2177113FECD400BF472F /* venncommand.cpp */,
767                         );
768                         name = commands;
769                         sourceTree = "<group>";
770                 };
771                 A7CB594211402F430010EB83 /* containers */ = {
772                         isa = PBXGroup;
773                         children = (
774                                 A7DA1FF3113FECD400BF472F /* alignmentcell.hpp */,
775                                 A7DA1FF2113FECD400BF472F /* alignmentcell.cpp */,
776                                 A7DA1FF4113FECD400BF472F /* alignmentdb.cpp */,
777                                 A7DA1FF5113FECD400BF472F /* alignmentdb.h */,
778                                 A7DA2001113FECD400BF472F /* blastdb.cpp */,
779                                 A7DA2002113FECD400BF472F /* blastdb.hpp */,
780                                 A7DA2035113FECD400BF472F /* database.cpp */,
781                                 A7DA2036113FECD400BF472F /* database.hpp */,
782                                 A7DA2037113FECD400BF472F /* datavector.hpp */,
783                                 A7DA2040113FECD400BF472F /* distancedb.cpp */,
784                                 A7DA2041113FECD400BF472F /* distancedb.hpp */,
785                                 A7DA204A113FECD400BF472F /* fastamap.cpp */,
786                                 A7DA204B113FECD400BF472F /* fastamap.h */,
787                                 A7DA2056113FECD400BF472F /* fullmatrix.cpp */,
788                                 A7DA2057113FECD400BF472F /* fullmatrix.h */,
789                                 A7DA2070113FECD400BF472F /* groupmap.cpp */,
790                                 A7DA2071113FECD400BF472F /* groupmap.h */,
791                                 A7DA2085113FECD400BF472F /* kmer.cpp */,
792                                 A7DA2086113FECD400BF472F /* kmer.hpp */,
793                                 A7DA2087113FECD400BF472F /* kmerdb.cpp */,
794                                 A7DA2088113FECD400BF472F /* kmerdb.hpp */,
795                                 A7DA2091113FECD400BF472F /* listvector.cpp */,
796                                 A7DA2092113FECD400BF472F /* listvector.hpp */,
797                                 A7DA20A2113FECD400BF472F /* nameassignment.cpp */,
798                                 A7DA20A3113FECD400BF472F /* nameassignment.hpp */,
799                                 A7DA20B6113FECD400BF472F /* ordervector.cpp */,
800                                 A7DA20B7113FECD400BF472F /* ordervector.hpp */,
801                                 A7DA20D2113FECD400BF472F /* rabundvector.cpp */,
802                                 A7DA20D3113FECD400BF472F /* rabundvector.hpp */,
803                                 A7DA20F6113FECD400BF472F /* sabundvector.cpp */,
804                                 A7DA20F7113FECD400BF472F /* sabundvector.hpp */,
805                                 A7DA20FE113FECD400BF472F /* sequence.cpp */,
806                                 A7DA20FF113FECD400BF472F /* sequence.hpp */,
807                                 A7DA2100113FECD400BF472F /* sequencedb.cpp */,
808                                 A7DA2101113FECD400BF472F /* sequencedb.h */,
809                                 A7DA2121113FECD400BF472F /* sharedlistvector.cpp */,
810                                 A7DA2122113FECD400BF472F /* sharedlistvector.h */,
811                                 A7DA212A113FECD400BF472F /* sharedordervector.cpp */,
812                                 A7DA212B113FECD400BF472F /* sharedordervector.h */,
813                                 A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */,
814                                 A7DA212D113FECD400BF472F /* sharedrabundvector.h */,
815                                 A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
816                                 A7DA212F113FECD400BF472F /* sharedsabundvector.h */,
817                                 A7DA214C113FECD400BF472F /* sparsematrix.cpp */,
818                                 A7DA214D113FECD400BF472F /* sparsematrix.hpp */,
819                                 A7DA214E113FECD400BF472F /* suffixdb.cpp */,
820                                 A7DA214F113FECD400BF472F /* suffixdb.hpp */,
821                                 A7DA2150113FECD400BF472F /* suffixnodes.cpp */,
822                                 A7DA2151113FECD400BF472F /* suffixnodes.hpp */,
823                                 A7DA2152113FECD400BF472F /* suffixtree.cpp */,
824                                 A7DA2153113FECD400BF472F /* suffixtree.hpp */,
825                                 A7DA215E113FECD400BF472F /* tree.cpp */,
826                                 A7DA215F113FECD400BF472F /* tree.h */,
827                                 A7DA2163113FECD400BF472F /* treemap.cpp */,
828                                 A7DA2164113FECD400BF472F /* treemap.h */,
829                                 A7DA2165113FECD400BF472F /* treenode.cpp */,
830                                 A7DA2166113FECD400BF472F /* treenode.h */,
831                         );
832                         name = containers;
833                         sourceTree = "<group>";
834                 };
835                 A7CB594511402F6E0010EB83 /* classifers */ = {
836                         isa = PBXGroup;
837                         children = (
838                                 A7DA201B113FECD400BF472F /* classify.cpp */,
839                                 A7DA201C113FECD400BF472F /* classify.h */,
840                                 A7DA1FF7113FECD400BF472F /* bayesian.cpp */,
841                                 A7DA1FF8113FECD400BF472F /* bayesian.h */,
842                                 A7DA2089113FECD400BF472F /* knn.cpp */,
843                                 A7DA208A113FECD400BF472F /* knn.h */,
844                                 A7DA20C4113FECD400BF472F /* phylotree.cpp */,
845                                 A7DA20C5113FECD400BF472F /* phylotree.h */,
846                                 A76AAD02117F322B003D8DA1 /* phylosummary.h */,
847                                 A76AAD03117F322B003D8DA1 /* phylosummary.cpp */,
848                                 A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */,
849                                 A7DA215D113FECD400BF472F /* taxonomyequalizer.h */,
850                         );
851                         name = classifers;
852                         sourceTree = "<group>";
853                 };
854                 A7CB594A11402FB40010EB83 /* chimeras */ = {
855                         isa = PBXGroup;
856                         children = (
857                                 A7DA2011113FECD400BF472F /* chimera.cpp */,
858                                 A7DA2012113FECD400BF472F /* chimera.h */,
859                                 A7DA1FF9113FECD400BF472F /* bellerophon.cpp */,
860                                 A7DA1FFA113FECD400BF472F /* bellerophon.h */,
861                                 A7DA200D113FECD400BF472F /* ccode.cpp */,
862                                 A7DA200E113FECD400BF472F /* ccode.h */,
863                                 A7DA2013113FECD400BF472F /* chimeracheckrdp.cpp */,
864                                 A7DA2014113FECD400BF472F /* chimeracheckrdp.h */,
865                                 A7DA2015113FECD400BF472F /* chimerarealigner.cpp */,
866                                 A7DA2016113FECD400BF472F /* chimerarealigner.h */,
867                                 A7DA2019113FECD400BF472F /* chimeraslayer.cpp */,
868                                 A7DA201A113FECD400BF472F /* chimeraslayer.h */,
869                                 A7DA2038113FECD400BF472F /* decalc.cpp */,
870                                 A7DA2039113FECD400BF472F /* decalc.h */,
871                                 A7DA2095113FECD400BF472F /* maligner.cpp */,
872                                 A7DA2096113FECD400BF472F /* maligner.h */,
873                                 A7DA20C8113FECD400BF472F /* pintail.cpp */,
874                                 A7DA20C9113FECD400BF472F /* pintail.h */,
875                                 A7DA2145113FECD400BF472F /* slayer.cpp */,
876                                 A7DA2146113FECD400BF472F /* slayer.h */,
877                         );
878                         name = chimeras;
879                         sourceTree = "<group>";
880                 };
881                 A7CB5953114033220010EB83 /* read */ = {
882                         isa = PBXGroup;
883                         children = (
884                                 A7DA2051113FECD400BF472F /* formatcolumn.cpp */,
885                                 A7DA2052113FECD400BF472F /* formatcolumn.h */,
886                                 A7DA2053113FECD400BF472F /* formatmatrix.h */,
887                                 A7DA2054113FECD400BF472F /* formatphylip.cpp */,
888                                 A7DA2055113FECD400BF472F /* formatphylip.h */,
889                                 A7DA20DF113FECD400BF472F /* readblast.cpp */,
890                                 A7DA20E0113FECD400BF472F /* readblast.h */,
891                                 A7DA20E1113FECD400BF472F /* readcluster.cpp */,
892                                 A7DA20E2113FECD400BF472F /* readcluster.h */,
893                                 A7DA20E3113FECD400BF472F /* readcolumn.cpp */,
894                                 A7DA20E4113FECD400BF472F /* readcolumn.h */,
895                                 A7DA20E7113FECD400BF472F /* readmatrix.hpp */,
896                                 A7DA20E8113FECD400BF472F /* readotu.cpp */,
897                                 A7DA20E9113FECD400BF472F /* readotu.h */,
898                                 A7DA20EC113FECD400BF472F /* readphylip.cpp */,
899                                 A7DA20ED113FECD400BF472F /* readphylip.h */,
900                                 A7DA20EE113FECD400BF472F /* readtree.cpp */,
901                                 A7DA20EF113FECD400BF472F /* readtree.h */,
902                         );
903                         name = read;
904                         sourceTree = "<group>";
905                 };
906 /* End PBXGroup section */
907
908 /* Begin PBXLegacyTarget section */
909                 D28A88AD04BDD90700651E21 /* mothur */ = {
910                         isa = PBXLegacyTarget;
911                         buildArgumentsString = "$(ACTION)";
912                         buildConfigurationList = 1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */;
913                         buildPhases = (
914                         );
915                         buildToolPath = /usr/bin/make;
916                         dependencies = (
917                         );
918                         name = mothur;
919                         passBuildSettingsInEnvironment = 1;
920                         productName = mothur;
921                 };
922 /* End PBXLegacyTarget section */
923
924 /* Begin PBXProject section */
925                 08FB7793FE84155DC02AAC07 /* Project object */ = {
926                         isa = PBXProject;
927                         attributes = {
928                                 BuildIndependentTargetsInParallel = YES;
929                         };
930                         buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
931                         compatibilityVersion = "Xcode 3.0";
932                         hasScannedForEncodings = 1;
933                         mainGroup = 08FB7794FE84155DC02AAC07 /* mothur */;
934                         projectDirPath = "";
935                         projectRoot = "";
936                         targets = (
937                                 D28A88AD04BDD90700651E21 /* mothur */,
938                         );
939                 };
940 /* End PBXProject section */
941
942 /* Begin XCBuildConfiguration section */
943                 1DEB919108733D9F0010E9CD /* Release */ = {
944                         isa = XCBuildConfiguration;
945                         buildSettings = {
946                                 COPY_PHASE_STRIP = YES;
947                                 GCC_ENABLE_FIX_AND_CONTINUE = NO;
948                                 OTHER_CFLAGS = "";
949                                 OTHER_LDFLAGS = "";
950                                 PRODUCT_NAME = mothur;
951                                 ZERO_LINK = NO;
952                         };
953                         name = Release;
954                 };
955                 1DEB919508733D9F0010E9CD /* Release */ = {
956                         isa = XCBuildConfiguration;
957                         buildSettings = {
958                                 ARCHS = (
959                                         ppc,
960                                         i386,
961                                 );
962                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
963                                 GCC_WARN_UNUSED_VARIABLE = YES;
964                                 LINK_WITH_STANDARD_LIBRARIES = YES;
965                                 PREBINDING = NO;
966                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
967                         };
968                         name = Release;
969                 };
970 /* End XCBuildConfiguration section */
971
972 /* Begin XCConfigurationList section */
973                 1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */ = {
974                         isa = XCConfigurationList;
975                         buildConfigurations = (
976                                 1DEB919108733D9F0010E9CD /* Release */,
977                         );
978                         defaultConfigurationIsVisible = 0;
979                         defaultConfigurationName = Release;
980                 };
981                 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
982                         isa = XCConfigurationList;
983                         buildConfigurations = (
984                                 1DEB919508733D9F0010E9CD /* Release */,
985                         );
986                         defaultConfigurationIsVisible = 0;
987                         defaultConfigurationName = Release;
988                 };
989 /* End XCConfigurationList section */
990         };
991         rootObject = 08FB7793FE84155DC02AAC07 /* Project object */;
992 }