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broke apart read matrix file
[mothur.git] / Mothur.xcodeproj / project.pbxproj
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212                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = "<group>"; };
213                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtree.h; sourceTree = "<group>"; };
214                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
215                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobscollectsummary.h; sourceTree = "<group>"; };
216                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = "<group>"; };
217                 37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = "<group>"; };
218                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
219                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = "<group>"; };
220                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = "<group>"; };
221                 37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
222                 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
223                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = "<group>"; };
224                 37D927BB0F21331F001D4494 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = "<group>"; };
225                 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = "<group>"; };
226                 37D927BD0F21331F001D4494 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = "<group>"; };
227                 37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = "<group>"; };
228                 37D927BF0F21331F001D4494 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = "<group>"; };
229                 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = "<group>"; };
230                 37D927C10F21331F001D4494 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = "<group>"; };
231                 37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = "<group>"; };
232                 37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = "<group>"; };
233                 37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = "<group>"; };
234                 37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = "<group>"; };
235                 37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = "<group>"; };
236                 37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = "<group>"; };
237                 37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = "<group>"; };
238                 37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = "<group>"; };
239                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = "<group>"; };
240                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = "<group>"; };
241                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = "<group>"; };
242                 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = "<group>"; };
243                 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = "<group>"; };
244                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = "<group>"; };
245                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = "<group>"; };
246                 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = "<group>"; };
247                 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = "<group>"; };
248                 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = "<group>"; };
249                 37D927D50F21331F001D4494 /* datavector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = datavector.hpp; sourceTree = "<group>"; };
250                 37D927D60F21331F001D4494 /* display.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = display.h; sourceTree = "<group>"; };
251                 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = "<group>"; };
252                 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = "<group>"; };
253                 37D927D90F21331F001D4494 /* errorchecking.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = errorchecking.cpp; sourceTree = "<group>"; };
254                 37D927DA0F21331F001D4494 /* errorchecking.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = errorchecking.h; sourceTree = "<group>"; };
255                 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = "<group>"; };
256                 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = "<group>"; };
257                 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = "<group>"; };
258                 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = "<group>"; };
259                 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = "<group>"; };
260                 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = "<group>"; };
261                 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = "<group>"; };
262                 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = "<group>"; };
263                 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = "<group>"; };
264                 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = "<group>"; };
265                 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = "<group>"; };
266                 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = "<group>"; };
267                 37D927E70F21331F001D4494 /* jackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = jackknife.cpp; sourceTree = "<group>"; };
268                 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = "<group>"; };
269                 37D927E90F21331F001D4494 /* kmer.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmer.cpp; sourceTree = "<group>"; };
270                 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = "<group>"; };
271                 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = "<group>"; };
272                 37D927EC0F21331F001D4494 /* kmerdb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmerdb.hpp; sourceTree = "<group>"; };
273                 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = "<group>"; };
274                 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = "<group>"; };
275                 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = "<group>"; };
276                 37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = "<group>"; };
277                 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = "<group>"; };
278                 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = "<group>"; };
279                 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = "<group>"; };
280                 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = "<group>"; };
281                 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = "<group>"; };
282                 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = "<group>"; };
283                 37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = "<group>"; };
284                 37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = "<group>"; };
285                 37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = "<group>"; };
286                 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = "<group>"; };
287                 37D927FD0F21331F001D4494 /* quitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = quitcommand.cpp; sourceTree = "<group>"; };
288                 37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = "<group>"; };
289                 37D927FF0F21331F001D4494 /* rabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rabundvector.cpp; sourceTree = "<group>"; };
290                 37D928000F21331F001D4494 /* rabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = rabundvector.hpp; sourceTree = "<group>"; };
291                 37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = "<group>"; };
292                 37D928020F21331F001D4494 /* rarecalc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarecalc.h; sourceTree = "<group>"; };
293                 37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = "<group>"; };
294                 37D928040F21331F001D4494 /* raredisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = raredisplay.h; sourceTree = "<group>"; };
295                 37D928050F21331F001D4494 /* rarefact.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefact.cpp; sourceTree = "<group>"; };
296                 37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = "<group>"; };
297                 37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = "<group>"; };
298                 37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = "<group>"; };
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300                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
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302                 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
303                 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
304                 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
305                 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = "<group>"; };
306                 37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = "<group>"; };
307                 37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = "<group>"; };
308                 37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = "<group>"; };
309                 37D928200F21331F001D4494 /* shared.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shared.cpp; sourceTree = "<group>"; };
310                 37D928210F21331F001D4494 /* shared.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shared.h; sourceTree = "<group>"; };
311                 37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
312                 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
313                 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = "<group>"; };
314                 37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = "<group>"; };
315                 37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = "<group>"; };
316                 37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = "<group>"; };
317                 37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = "<group>"; };
318                 37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = "<group>"; };
319                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = "<group>"; };
320                 37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = "<group>"; };
321                 37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = "<group>"; };
322                 37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = "<group>"; };
323                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = "<group>"; };
324                 37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = "<group>"; };
325                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = "<group>"; };
326                 37D928310F21331F001D4494 /* sharedrabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundvector.h; sourceTree = "<group>"; };
327                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = "<group>"; };
328                 37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = "<group>"; };
329                 37D928340F21331F001D4494 /* sharedsobs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobs.cpp; sourceTree = "<group>"; };
330                 37D928350F21331F001D4494 /* sharedsobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsobs.h; sourceTree = "<group>"; };
331                 37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = "<group>"; };
332                 37D928370F21331F001D4494 /* sharedsorabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorabund.h; sourceTree = "<group>"; };
333                 37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = "<group>"; };
334                 37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = "<group>"; };
335                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = "<group>"; };
336                 37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = "<group>"; };
337                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = "<group>"; };
338                 37D9283D0F21331F001D4494 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = "<group>"; };
339                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = "<group>"; };
340                 37D9283F0F21331F001D4494 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = "<group>"; };
341                 37D928400F21331F001D4494 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = "<group>"; };
342                 37D928410F21331F001D4494 /* simpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpson.h; sourceTree = "<group>"; };
343                 37D928420F21331F001D4494 /* singlelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = singlelinkage.cpp; sourceTree = "<group>"; };
344                 37D928430F21331F001D4494 /* sobs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sobs.h; sourceTree = "<group>"; };
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351                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
352                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = "<group>"; };
353                 37D9284D0F21331F001D4494 /* uvest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = uvest.cpp; sourceTree = "<group>"; };
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356                 37D928500F21331F001D4494 /* validcalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = validcalculator.h; sourceTree = "<group>"; };
357                 37D928510F21331F001D4494 /* validcommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = validcommands.cpp; sourceTree = "<group>"; };
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363                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treenode.cpp; sourceTree = "<group>"; };
364                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readtreecommand.h; sourceTree = "<group>"; };
365                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtreecommand.cpp; sourceTree = "<group>"; };
366                 7E412F420F8D213C00381DD0 /* libshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuff.h; sourceTree = "<group>"; };
367                 7E412F470F8D21B600381DD0 /* slibshuff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = slibshuff.h; sourceTree = "<group>"; };
368                 7E412F480F8D21B600381DD0 /* slibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = slibshuff.cpp; sourceTree = "<group>"; };
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370                 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dlibshuff.cpp; sourceTree = "<group>"; };
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377                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = "<group>"; };
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388                 EB6F01590F6AC1670048081A /* sharedbdiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbdiversity.h; sourceTree = "<group>"; };
389                 EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbdiversity.cpp; sourceTree = "<group>"; };
390                 EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
391                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
392                 EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = "<group>"; };
393                 EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = "<group>"; };
394 /* End PBXFileReference section */
395
396 /* Begin PBXFrameworksBuildPhase section */
397                 8DD76F660486A84900D96B5E /* Frameworks */ = {
398                         isa = PBXFrameworksBuildPhase;
399                         buildActionMask = 2147483647;
400                         files = (
401                         );
402                         runOnlyForDeploymentPostprocessing = 0;
403                 };
404 /* End PBXFrameworksBuildPhase section */
405
406 /* Begin PBXGroup section */
407                 08FB7794FE84155DC02AAC07 /* Mothur */ = {
408                         isa = PBXGroup;
409                         children = (
410                                 08FB7795FE84155DC02AAC07 /* Source */,
411                                 C6859E8C029090F304C91782 /* Documentation */,
412                                 1AB674ADFE9D54B511CA2CBB /* Products */,
413                         );
414                         name = Mothur;
415                         sourceTree = "<group>";
416                 };
417                 08FB7795FE84155DC02AAC07 /* Source */ = {
418                         isa = PBXGroup;
419                         children = (
420                                 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
421                                 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
422                                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
423                                 37D928A60F2133C0001D4494 /* calculators */,
424                                 37D927C20F21331F001D4494 /* cluster.hpp */,
425                                 37D927C10F21331F001D4494 /* cluster.cpp */,
426                                 7E412F470F8D21B600381DD0 /* slibshuff.h */,
427                                 7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
428                                 7E412F420F8D213C00381DD0 /* libshuff.h */,
429                                 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
430                                 37D928A90F2133E5001D4494 /* commands */,
431                                 37D927C60F21331F001D4494 /* collect.h */,
432                                 37D927C50F21331F001D4494 /* collect.cpp */,
433                                 37D927C90F21331F001D4494 /* collectdisplay.h */,
434                                 37D928AC0F213420001D4494 /* containers */,
435                                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */,
436                                 37D927CF0F21331F001D4494 /* commandfactory.hpp */,
437                                 372E12EC0F264D320095CF7E /* commandfactory.cpp */,
438                                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
439                                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
440                                 37D927D20F21331F001D4494 /* completelinkage.cpp */,
441                                 37D927D40F21331F001D4494 /* database.hpp */,
442                                 37D927D30F21331F001D4494 /* database.cpp */,
443                                 37D927D60F21331F001D4494 /* display.h */,
444                                 37D927D80F21331F001D4494 /* engine.hpp */,
445                                 37D927D70F21331F001D4494 /* engine.cpp */,
446                                 37D928B10F213472001D4494 /* errorcheckor */,
447                                 37D927DE0F21331F001D4494 /* fileoutput.h */,
448                                 37D927DD0F21331F001D4494 /* fileoutput.cpp */,
449                                 37D927E00F21331F001D4494 /* globaldata.hpp */,
450                                 37D927DF0F21331F001D4494 /* globaldata.cpp */,
451                                 375873ED0F7D646F0040F377 /* heatmap.h */,
452                                 375873EE0F7D646F0040F377 /* heatmap.cpp */,
453                                 37D927E60F21331F001D4494 /* inputdata.h */,
454                                 37D927E50F21331F001D4494 /* inputdata.cpp */,
455                                 37D927EA0F21331F001D4494 /* kmer.hpp */,
456                                 37D927E90F21331F001D4494 /* kmer.cpp */,
457                                 37D927EC0F21331F001D4494 /* kmerdb.hpp */,
458                                 37D927EB0F21331F001D4494 /* kmerdb.cpp */,
459                                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
460                                 37D927EF0F21331F001D4494 /* mothur.cpp */,
461                                 37D927F10F21331F001D4494 /* nameassignment.hpp */,
462                                 37D927F00F21331F001D4494 /* nameassignment.cpp */,
463                                 37D927F60F21331F001D4494 /* observable.h */,
464                                 37D927FC0F21331F001D4494 /* progress.hpp */,
465                                 37D927FB0F21331F001D4494 /* progress.cpp */,
466                                 37D928040F21331F001D4494 /* raredisplay.h */,
467                                 37D928030F21331F001D4494 /* raredisplay.cpp */,
468                                 37D928060F21331F001D4494 /* rarefact.h */,
469                                 37D928050F21331F001D4494 /* rarefact.cpp */,
470                                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
471                                 375AA1340F9E433D008EF9B8 /* readcolumn.h */,
472                                 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
473                                 37D928130F21331F001D4494 /* readmatrix.hpp */,
474                                 375AA1360F9E433D008EF9B8 /* readotu.h */,
475                                 375AA1350F9E433D008EF9B8 /* readotu.cpp */,
476                                 375AA1380F9E433D008EF9B8 /* readphylip.h */,
477                                 375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
478                                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
479                                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
480                                 37D9281D0F21331F001D4494 /* sequence.hpp */,
481                                 37D9281C0F21331F001D4494 /* sequence.cpp */,
482                                 37D928210F21331F001D4494 /* shared.h */,
483                                 37D928200F21331F001D4494 /* shared.cpp */,
484                                 211C38310F961DD400FEE541 /* sharedutilities.h */,
485                                 211C38300F961DD400FEE541 /* sharedutilities.cpp */,
486                                 37D928420F21331F001D4494 /* singlelinkage.cpp */,
487                                 37D928480F21331F001D4494 /* summarydata.h */,
488                                 37D928490F21331F001D4494 /* summarydisplay.h */,
489                                 37519AB30F810FAE00FED5E8 /* venn.h */,
490                                 37519AB40F810FAE00FED5E8 /* venn.cpp */,
491                         );
492                         name = Source;
493                         sourceTree = "<group>";
494                 };
495                 1AB674ADFE9D54B511CA2CBB /* Products */ = {
496                         isa = PBXGroup;
497                         children = (
498                                 8DD76F6C0486A84900D96B5E /* mothur */,
499                         );
500                         name = Products;
501                         sourceTree = "<group>";
502                 };
503                 37D928A60F2133C0001D4494 /* calculators */ = {
504                         isa = PBXGroup;
505                         children = (
506                                 37D927BE0F21331F001D4494 /* calculator.h */,
507                                 3792948D0F2E271100B9034A /* treecalculator.h */,
508                                 37D927BD0F21331F001D4494 /* calculator.cpp */,
509                                 37D927B90F21331F001D4494 /* ace.h */,
510                                 37D927B80F21331F001D4494 /* ace.cpp */,
511                                 EB1216860F619B83004A865F /* bergerparker.h */,
512                                 EB1216870F619B83004A865F /* bergerparker.cpp */,
513                                 37D927BC0F21331F001D4494 /* bootstrap.h */,
514                                 37D927BB0F21331F001D4494 /* bootstrap.cpp */,
515                                 EB1216E30F61ACFB004A865F /* bstick.h */,
516                                 EB1216E40F61ACFB004A865F /* bstick.cpp */,
517                                 37D927C00F21331F001D4494 /* chao1.h */,
518                                 37D927BF0F21331F001D4494 /* chao1.cpp */,
519                                 EB9303F70F53517300E8EF26 /* geom.h */,
520                                 EB9303F80F53517300E8EF26 /* geom.cpp */,
521                                 EB9303E90F534D9400E8EF26 /* logsd.h */,
522                                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
523                                 EB6E68170F5F1C780044E17B /* qstat.h */,
524                                 EB6E68180F5F1C780044E17B /* qstat.cpp */,
525                                 37D927E80F21331F001D4494 /* jackknife.h */,
526                                 37D927E70F21331F001D4494 /* jackknife.cpp */,
527                                 375873F90F7D64AB0040F377 /* nseqs.h */,
528                                 37D927F50F21331F001D4494 /* npshannon.h */,
529                                 37D927F40F21331F001D4494 /* npshannon.cpp */,
530                                 379294880F2E258500B9034A /* parsimony.h */,
531                                 379294890F2E258500B9034A /* parsimony.cpp */,
532                                 37D928020F21331F001D4494 /* rarecalc.h */,
533                                 37D928010F21331F001D4494 /* rarecalc.cpp */,
534                                 37D9281F0F21331F001D4494 /* shannon.h */,
535                                 37D9281E0F21331F001D4494 /* shannon.cpp */,
536                                 37D928230F21331F001D4494 /* sharedace.h */,
537                                 37D928220F21331F001D4494 /* sharedace.cpp */,
538                                 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
539                                 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
540                                 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
541                                 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
542                                 EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
543                                 EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */,
544                                 37D928250F21331F001D4494 /* sharedchao1.h */,
545                                 37D928240F21331F001D4494 /* sharedchao1.cpp */,
546                                 37D928290F21331F001D4494 /* sharedjabund.h */,
547                                 37D928280F21331F001D4494 /* sharedjabund.cpp */,
548                                 37D9282B0F21331F001D4494 /* sharedjclass.h */,
549                                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
550                                 37D9282D0F21331F001D4494 /* sharedjest.h */,
551                                 37D9282C0F21331F001D4494 /* sharedjest.cpp */,
552                                 EB1217210F61C9AC004A865F /* sharedkstest.h */,
553                                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
554                                 375874000F7D64EF0040F377 /* sharedkulczynski.h */,
555                                 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
556                                 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
557                                 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
558                                 375874010F7D64EF0040F377 /* sharedlennon.h */,
559                                 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
560                                 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
561                                 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
562                                 375874090F7D64FC0040F377 /* sharedochiai.h */,
563                                 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
564                                 3758740A0F7D64FC0040F377 /* sharednseqs.h */,
565                                 37D928350F21331F001D4494 /* sharedsobs.h */,
566                                 37D928340F21331F001D4494 /* sharedsobs.cpp */,
567                                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
568                                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
569                                 37D928370F21331F001D4494 /* sharedsorabund.h */,
570                                 37D928360F21331F001D4494 /* sharedsorabund.cpp */,
571                                 37D928390F21331F001D4494 /* sharedsorclass.h */,
572                                 37D928380F21331F001D4494 /* sharedsorclass.cpp */,
573                                 37D9283B0F21331F001D4494 /* sharedsorest.h */,
574                                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
575                                 37D9283D0F21331F001D4494 /* sharedthetan.h */,
576                                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
577                                 37D9283F0F21331F001D4494 /* sharedthetayc.h */,
578                                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
579                                 37D928410F21331F001D4494 /* simpson.h */,
580                                 37D928400F21331F001D4494 /* simpson.cpp */,
581                                 37D928430F21331F001D4494 /* sobs.h */,
582                                 374610810F40652400460C57 /* unweighted.h */,
583                                 374610820F40652400460C57 /* unweighted.cpp */,
584                                 37D9284E0F21331F001D4494 /* uvest.h */,
585                                 37D9284D0F21331F001D4494 /* uvest.cpp */,
586                                 3746107C0F4064D100460C57 /* weighted.h */,
587                                 3746107D0F4064D100460C57 /* weighted.cpp */,
588                         );
589                         name = calculators;
590                         sourceTree = "<group>";
591                 };
592                 37D928A90F2133E5001D4494 /* commands */ = {
593                         isa = PBXGroup;
594                         children = (
595                                 37D927CD0F21331F001D4494 /* command.hpp */,
596                                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
597                                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
598                                 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
599                                 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
600                                 37D927C40F21331F001D4494 /* clustercommand.h */,
601                                 37D927C30F21331F001D4494 /* clustercommand.cpp */,
602                                 37D927C80F21331F001D4494 /* collectcommand.h */,
603                                 37D927C70F21331F001D4494 /* collectcommand.cpp */,
604                                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
605                                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
606                                 37B28F660F27590100808A62 /* deconvolutecommand.h */,
607                                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
608                                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
609                                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
610                                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
611                                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
612                                 A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
613                                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
614                                 370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
615                                 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
616                                 375873F10F7D64800040F377 /* heatmapcommand.h */,
617                                 375873F00F7D64800040F377 /* heatmapcommand.cpp */,
618                                 37D927E40F21331F001D4494 /* helpcommand.h */,
619                                 37D927E30F21331F001D4494 /* helpcommand.cpp */,
620                                 375873F40F7D648F0040F377 /* libshuffcommand.h */,
621                                 375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
622                                 375873F60F7D649C0040F377 /* nocommands.cpp */,
623                                 375873F70F7D649C0040F377 /* nocommands.h */,
624                                 37D927FA0F21331F001D4494 /* parselistcommand.h */,
625                                 37D927F90F21331F001D4494 /* parselistcommand.cpp */,
626                                 3792946E0F2E191800B9034A /* parsimonycommand.h */,
627                                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
628                                 37D927FE0F21331F001D4494 /* quitcommand.h */,
629                                 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
630                                 37D928080F21331F001D4494 /* rarefactcommand.h */,
631                                 37D928070F21331F001D4494 /* rarefactcommand.cpp */,
632                                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
633                                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
634                                 372E12940F263D5A0095CF7E /* readdistcommand.h */,
635                                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
636                                 372E126E0F26365B0095CF7E /* readotucommand.h */,
637                                 372E126F0F26365B0095CF7E /* readotucommand.cpp */,
638                                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
639                                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
640                                 37D928270F21331F001D4494 /* sharedcommand.h */,
641                                 37D928260F21331F001D4494 /* sharedcommand.cpp */,
642                                 37D928470F21331F001D4494 /* summarycommand.h */,
643                                 37D928460F21331F001D4494 /* summarycommand.cpp */,
644                                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
645                                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
646                                 211C38370F961E1F00FEE541 /* treegroupscommand.h */,
647                                 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
648                                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
649                                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
650                                 374610760F40645300460C57 /* unifracweightedcommand.h */,
651                                 374610770F40645300460C57 /* unifracweightedcommand.cpp */,
652                                 37519A9F0F810D0200FED5E8 /* venncommand.h */,
653                                 37519AA00F810D0200FED5E8 /* venncommand.cpp */,
654                         );
655                         name = commands;
656                         sourceTree = "<group>";
657                 };
658                 37D928AC0F213420001D4494 /* containers */ = {
659                         isa = PBXGroup;
660                         children = (
661                                 37D927D50F21331F001D4494 /* datavector.hpp */,
662                                 37D927DC0F21331F001D4494 /* fastamap.h */,
663                                 37D927DB0F21331F001D4494 /* fastamap.cpp */,
664                                 375873EA0F7D64520040F377 /* fullmatrix.h */,
665                                 375873EB0F7D64520040F377 /* fullmatrix.cpp */,
666                                 37D927E20F21331F001D4494 /* groupmap.h */,
667                                 37D927E10F21331F001D4494 /* groupmap.cpp */,
668                                 37D927EE0F21331F001D4494 /* listvector.hpp */,
669                                 37D927ED0F21331F001D4494 /* listvector.cpp */,
670                                 37D927F80F21331F001D4494 /* ordervector.hpp */,
671                                 37D927F70F21331F001D4494 /* ordervector.cpp */,
672                                 37D928000F21331F001D4494 /* rabundvector.hpp */,
673                                 37D927FF0F21331F001D4494 /* rabundvector.cpp */,
674                                 37D9281B0F21331F001D4494 /* sabundvector.hpp */,
675                                 37D9281A0F21331F001D4494 /* sabundvector.cpp */,
676                                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
677                                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
678                                 37D9282F0F21331F001D4494 /* sharedordervector.h */,
679                                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
680                                 37D928310F21331F001D4494 /* sharedrabundvector.h */,
681                                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
682                                 37D928330F21331F001D4494 /* sharedsabundvector.h */,
683                                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
684                                 37D928450F21331F001D4494 /* sparsematrix.hpp */,
685                                 37D928440F21331F001D4494 /* sparsematrix.cpp */,
686                                 37AD4DB90F28E2FE00AA2D49 /* tree.h */,
687                                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
688                                 379293C10F2DE73400B9034A /* treemap.h */,
689                                 379293C20F2DE73400B9034A /* treemap.cpp */,
690                                 37E5F3E10F29FD4200F8D827 /* treenode.h */,
691                                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
692                         );
693                         name = containers;
694                         sourceTree = "<group>";
695                 };
696                 37D928B10F213472001D4494 /* errorcheckor */ = {
697                         isa = PBXGroup;
698                         children = (
699                                 37D927DA0F21331F001D4494 /* errorchecking.h */,
700                                 37D927D90F21331F001D4494 /* errorchecking.cpp */,
701                                 37D928500F21331F001D4494 /* validcalculator.h */,
702                                 37D9284F0F21331F001D4494 /* validcalculator.cpp */,
703                                 37D928520F21331F001D4494 /* validcommands.h */,
704                                 37D928510F21331F001D4494 /* validcommands.cpp */,
705                                 37D928540F21331F001D4494 /* validparameter.h */,
706                                 37D928530F21331F001D4494 /* validparameter.cpp */,
707                         );
708                         name = errorcheckor;
709                         sourceTree = "<group>";
710                 };
711                 C6859E8C029090F304C91782 /* Documentation */ = {
712                         isa = PBXGroup;
713                         children = (
714                                 C6859E8B029090EE04C91782 /* Mothur.1 */,
715                         );
716                         name = Documentation;
717                         sourceTree = "<group>";
718                 };
719 /* End PBXGroup section */
720
721 /* Begin PBXNativeTarget section */
722                 8DD76F620486A84900D96B5E /* mothur */ = {
723                         isa = PBXNativeTarget;
724                         buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
725                         buildPhases = (
726                                 8DD76F640486A84900D96B5E /* Sources */,
727                                 8DD76F660486A84900D96B5E /* Frameworks */,
728                                 8DD76F690486A84900D96B5E /* CopyFiles */,
729                         );
730                         buildRules = (
731                         );
732                         dependencies = (
733                         );
734                         name = mothur;
735                         productInstallPath = "$(HOME)/bin";
736                         productName = Mothur;
737                         productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
738                         productType = "com.apple.product-type.tool";
739                 };
740 /* End PBXNativeTarget section */
741
742 /* Begin PBXProject section */
743                 08FB7793FE84155DC02AAC07 /* Project object */ = {
744                         isa = PBXProject;
745                         buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
746                         compatibilityVersion = "Xcode 3.0";
747                         hasScannedForEncodings = 1;
748                         mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */;
749                         projectDirPath = "";
750                         projectRoot = "";
751                         targets = (
752                                 8DD76F620486A84900D96B5E /* mothur */,
753                         );
754                 };
755 /* End PBXProject section */
756
757 /* Begin PBXSourcesBuildPhase section */
758                 8DD76F640486A84900D96B5E /* Sources */ = {
759                         isa = PBXSourcesBuildPhase;
760                         buildActionMask = 2147483647;
761                         files = (
762                                 37D928550F21331F001D4494 /* ace.cpp in Sources */,
763                                 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */,
764                                 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */,
765                                 37D928580F21331F001D4494 /* calculator.cpp in Sources */,
766                                 37D928590F21331F001D4494 /* chao1.cpp in Sources */,
767                                 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */,
768                                 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */,
769                                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
770                                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
771                                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
772                                 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */,
773                                 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
774                                 37D928620F21331F001D4494 /* database.cpp in Sources */,
775                                 37D928630F21331F001D4494 /* engine.cpp in Sources */,
776                                 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */,
777                                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
778                                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
779                                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
780                                 37D928680F21331F001D4494 /* groupmap.cpp in Sources */,
781                                 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */,
782                                 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */,
783                                 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */,
784                                 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */,
785                                 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */,
786                                 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
787                                 37D9286F0F21331F001D4494 /* mothur.cpp in Sources */,
788                                 37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
789                                 37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
790                                 37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
791                                 37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */,
792                                 37D928750F21331F001D4494 /* progress.cpp in Sources */,
793                                 37D928760F21331F001D4494 /* quitcommand.cpp in Sources */,
794                                 37D928770F21331F001D4494 /* rabundvector.cpp in Sources */,
795                                 37D928780F21331F001D4494 /* rarecalc.cpp in Sources */,
796                                 37D928790F21331F001D4494 /* raredisplay.cpp in Sources */,
797                                 37D9287A0F21331F001D4494 /* rarefact.cpp in Sources */,
798                                 37D9287B0F21331F001D4494 /* rarefactcommand.cpp in Sources */,
799                                 37D9287C0F21331F001D4494 /* rarefactsharedcommand.cpp in Sources */,
800                                 37D928840F21331F001D4494 /* sabundvector.cpp in Sources */,
801                                 37D928850F21331F001D4494 /* sequence.cpp in Sources */,
802                                 37D928860F21331F001D4494 /* shannon.cpp in Sources */,
803                                 37D928870F21331F001D4494 /* shared.cpp in Sources */,
804                                 37D928880F21331F001D4494 /* sharedace.cpp in Sources */,
805                                 37D928890F21331F001D4494 /* sharedchao1.cpp in Sources */,
806                                 37D9288A0F21331F001D4494 /* sharedcommand.cpp in Sources */,
807                                 37D9288B0F21331F001D4494 /* sharedjabund.cpp in Sources */,
808                                 37D9288C0F21331F001D4494 /* sharedjclass.cpp in Sources */,
809                                 37D9288D0F21331F001D4494 /* sharedjest.cpp in Sources */,
810                                 37D9288E0F21331F001D4494 /* sharedordervector.cpp in Sources */,
811                                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */,
812                                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */,
813                                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */,
814                                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */,
815                                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */,
816                                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */,
817                                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */,
818                                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */,
819                                 37D928970F21331F001D4494 /* simpson.cpp in Sources */,
820                                 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */,
821                                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */,
822                                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */,
823                                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */,
824                                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */,
825                                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */,
826                                 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */,
827                                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */,
828                                 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */,
829                                 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */,
830                                 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */,
831                                 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */,
832                                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */,
833                                 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */,
834                                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */,
835                                 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
836                                 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
837                                 379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
838                                 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */,
839                                 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
840                                 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
841                                 3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
842                                 374610830F40652400460C57 /* unweighted.cpp in Sources */,
843                                 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
844                                 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
845                                 A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
846                                 A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
847                                 A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
848                                 EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */,
849                                 EB9303F90F53517300E8EF26 /* geom.cpp in Sources */,
850                                 EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */,
851                                 EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
852                                 EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
853                                 EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
854                                 EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */,
855                                 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
856                                 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
857                                 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */,
858                                 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */,
859                                 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */,
860                                 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */,
861                                 375874040F7D64EF0040F377 /* sharedkulczynski.cpp in Sources */,
862                                 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */,
863                                 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */,
864                                 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */,
865                                 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */,
866                                 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */,
867                                 37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */,
868                                 37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */,
869                                 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */,
870                                 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */,
871                                 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */,
872                                 7E412FEA0F8D3E2C00381DD0 /* libshuff.cpp in Sources */,
873                                 7E4130F80F8E58FA00381DD0 /* dlibshuff.cpp in Sources */,
874                                 211C38320F961DD400FEE541 /* sharedutilities.cpp in Sources */,
875                                 211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */,
876                                 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */,
877                                 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */,
878                                 375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */,
879                                 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
880                         );
881                         runOnlyForDeploymentPostprocessing = 0;
882                 };
883 /* End PBXSourcesBuildPhase section */
884
885 /* Begin XCBuildConfiguration section */
886                 1DEB923208733DC60010E9CD /* Debug */ = {
887                         isa = XCBuildConfiguration;
888                         buildSettings = {
889                                 COPY_PHASE_STRIP = NO;
890                                 GCC_DYNAMIC_NO_PIC = NO;
891                                 GCC_ENABLE_FIX_AND_CONTINUE = YES;
892                                 GCC_MODEL_TUNING = G5;
893                                 GCC_OPTIMIZATION_LEVEL = 0;
894                                 GCC_PREPROCESSOR_DEFINITIONS = (
895                                         "_GLIBCXX_DEBUG=1",
896                                         "_GLIBCXX_DEBUG_PEDANTIC=1",
897                                 );
898                                 INSTALL_PATH = /usr/local/bin;
899                                 PRODUCT_NAME = mothur;
900                                 ZERO_LINK = YES;
901                         };
902                         name = Debug;
903                 };
904                 1DEB923308733DC60010E9CD /* Release */ = {
905                         isa = XCBuildConfiguration;
906                         buildSettings = {
907                                 DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
908                                 GCC_MODEL_TUNING = G5;
909                                 INSTALL_PATH = /usr/local/bin;
910                                 PRODUCT_NAME = mothur;
911                         };
912                         name = Release;
913                 };
914                 1DEB923608733DC60010E9CD /* Debug */ = {
915                         isa = XCBuildConfiguration;
916                         buildSettings = {
917                                 GCC_OPTIMIZATION_LEVEL = 3;
918                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
919                                 GCC_WARN_UNUSED_VARIABLE = YES;
920                                 PREBINDING = NO;
921                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
922                         };
923                         name = Debug;
924                 };
925                 1DEB923708733DC60010E9CD /* Release */ = {
926                         isa = XCBuildConfiguration;
927                         buildSettings = {
928                                 ARCHS = (
929                                         ppc,
930                                         i386,
931                                 );
932                                 GCC_OPTIMIZATION_LEVEL = 3;
933                                 GCC_WARN_ABOUT_RETURN_TYPE = YES;
934                                 GCC_WARN_UNUSED_VARIABLE = YES;
935                                 PREBINDING = NO;
936                                 SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
937                         };
938                         name = Release;
939                 };
940 /* End XCBuildConfiguration section */
941
942 /* Begin XCConfigurationList section */
943                 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
944                         isa = XCConfigurationList;
945                         buildConfigurations = (
946                                 1DEB923208733DC60010E9CD /* Debug */,
947                                 1DEB923308733DC60010E9CD /* Release */,
948                         );
949                         defaultConfigurationIsVisible = 0;
950                         defaultConfigurationName = Release;
951                 };
952                 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
953                         isa = XCConfigurationList;
954                         buildConfigurations = (
955                                 1DEB923608733DC60010E9CD /* Debug */,
956                                 1DEB923708733DC60010E9CD /* Release */,
957                         );
958                         defaultConfigurationIsVisible = 0;
959                         defaultConfigurationName = Release;
960                 };
961 /* End XCConfigurationList section */
962         };
963         rootObject = 08FB7793FE84155DC02AAC07 /* Project object */;
964 }