Mothur.xcodeproj/project.pbxproj

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 219                 373C69290FC1C9EB00137ACD /* nastreport.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nastreport.cpp; sourceTree = "<group>"; };
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 223                 373C69960FC1E63600137ACD /* efron.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = efron.cpp; sourceTree = "<group>"; };
 224                 373C69970FC1E63600137ACD /* efron.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = efron.h; sourceTree = "<group>"; };
 225                 373C69980FC1E63600137ACD /* solow.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = solow.cpp; sourceTree = "<group>"; };
 226                 373C69990FC1E63600137ACD /* solow.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = solow.h; sourceTree = "<group>"; };
 227                 374610760F40645300460C57 /* unifracweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracweightedcommand.h; sourceTree = "<group>"; };
 228                 374610770F40645300460C57 /* unifracweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracweightedcommand.cpp; sourceTree = "<group>"; };
 229                 3746107C0F4064D100460C57 /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
 230                 3746107D0F4064D100460C57 /* weighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weighted.cpp; sourceTree = "<group>"; };
 231                 374610810F40652400460C57 /* unweighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unweighted.h; sourceTree = "<group>"; };
 232                 374610820F40652400460C57 /* unweighted.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unweighted.cpp; sourceTree = "<group>"; };
 233                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = unifracunweightedcommand.h; sourceTree = "<group>"; };
 234                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = unifracunweightedcommand.cpp; sourceTree = "<group>"; };
 235                 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = "<group>"; };
 236                 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = "<group>"; };
 237                 37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = "<group>"; };
 238                 37519AA00F810D0200FED5E8 /* venncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venncommand.cpp; sourceTree = "<group>"; };
 239                 37519AB30F810FAE00FED5E8 /* venn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venn.h; sourceTree = "<group>"; };
 240                 37519AB40F810FAE00FED5E8 /* venn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = venn.cpp; sourceTree = "<group>"; };
 241                 375873EA0F7D64520040F377 /* fullmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fullmatrix.h; sourceTree = "<group>"; };
 242                 375873EB0F7D64520040F377 /* fullmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fullmatrix.cpp; sourceTree = "<group>"; };
 243                 375873ED0F7D646F0040F377 /* heatmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmap.h; sourceTree = "<group>"; };
 244                 375873EE0F7D646F0040F377 /* heatmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmap.cpp; sourceTree = "<group>"; };
 245                 375873F00F7D64800040F377 /* heatmapcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapcommand.cpp; sourceTree = "<group>"; };
 246                 375873F10F7D64800040F377 /* heatmapcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapcommand.h; sourceTree = "<group>"; };
 247                 375873F30F7D648F0040F377 /* libshuffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = libshuffcommand.cpp; sourceTree = "<group>"; };
 248                 375873F40F7D648F0040F377 /* libshuffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = libshuffcommand.h; sourceTree = "<group>"; };
 249                 375873F60F7D649C0040F377 /* nocommands.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nocommands.cpp; sourceTree = "<group>"; };
 250                 375873F70F7D649C0040F377 /* nocommands.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nocommands.h; sourceTree = "<group>"; };
 251                 375873F90F7D64AB0040F377 /* nseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = nseqs.h; sourceTree = "<group>"; };
 252                 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbraycurtis.h; sourceTree = "<group>"; };
 253                 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbraycurtis.cpp; sourceTree = "<group>"; };
 254                 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynski.cpp; sourceTree = "<group>"; };
 255                 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlennon.cpp; sourceTree = "<group>"; };
 256                 375874000F7D64EF0040F377 /* sharedkulczynski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynski.h; sourceTree = "<group>"; };
 257                 375874010F7D64EF0040F377 /* sharedlennon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlennon.h; sourceTree = "<group>"; };
 258                 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkulczynskicody.cpp; sourceTree = "<group>"; };
 259                 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkulczynskicody.h; sourceTree = "<group>"; };
 260                 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmorisitahorn.h; sourceTree = "<group>"; };
 261                 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmorisitahorn.cpp; sourceTree = "<group>"; };
 262                 375874090F7D64FC0040F377 /* sharedochiai.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedochiai.h; sourceTree = "<group>"; };
 263                 3758740A0F7D64FC0040F377 /* sharednseqs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharednseqs.h; sourceTree = "<group>"; };
 264                 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedochiai.cpp; sourceTree = "<group>"; };
 265                 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readcolumn.cpp; sourceTree = "<group>"; };
 266                 375AA1340F9E433D008EF9B8 /* readcolumn.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readcolumn.h; sourceTree = "<group>"; };
 267                 375AA1350F9E433D008EF9B8 /* readotu.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readotu.cpp; sourceTree = "<group>"; };
 268                 375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = "<group>"; };
 269                 375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
 270                 375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
 271                 377326630FAF16E0007ABB8B /* concensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = concensuscommand.cpp; sourceTree = "<group>"; };
 272                 377326640FAF16E0007ABB8B /* concensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = concensuscommand.h; sourceTree = "<group>"; };
 273                 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = "<group>"; };
 274                 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = "<group>"; };
 275                 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = "<group>"; };
 276                 378C1AF10FB0644D004D63F5 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = "<group>"; };
 277                 378C1AF20FB0644D004D63F5 /* readclustal.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readclustal.cpp; sourceTree = "<group>"; };
 278                 378C1AF30FB0644D004D63F5 /* readclustal.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readclustal.h; sourceTree = "<group>"; };
 279                 378C1AF40FB0644D004D63F5 /* readfasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readfasta.cpp; sourceTree = "<group>"; };
 280                 378C1AF50FB0644D004D63F5 /* readfasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readfasta.h; sourceTree = "<group>"; };
 281                 378C1AF60FB0644D004D63F5 /* readnexus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readnexus.cpp; sourceTree = "<group>"; };
 282                 378C1AF70FB0644D004D63F5 /* readnexus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readnexus.h; sourceTree = "<group>"; };
 283                 378C1AF80FB0644D004D63F5 /* readnexusal.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readnexusal.h; sourceTree = "<group>"; };
 284                 378C1AFB0FB0644D004D63F5 /* readseqsphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readseqsphylip.cpp; sourceTree = "<group>"; };
 285                 378C1AFC0FB0644D004D63F5 /* readseqsphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readseqsphylip.h; sourceTree = "<group>"; };
 286                 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = "<group>"; };
 287                 378C1AFE0FB0644D004D63F5 /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = "<group>"; };
 288                 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = "<group>"; };
 289                 378C1B000FB0644D004D63F5 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = "<group>"; };
 290                 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = "<group>"; };
 291                 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = "<group>"; };
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 293                 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = aligncommand.cpp; sourceTree = "<group>"; };
 294                 379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
 295                 379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
 296                 3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
 297                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimonycommand.cpp; sourceTree = "<group>"; };
 298                 379294880F2E258500B9034A /* parsimony.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimony.h; sourceTree = "<group>"; };
 299                 379294890F2E258500B9034A /* parsimony.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsimony.cpp; sourceTree = "<group>"; };
 300                 3792948D0F2E271100B9034A /* treecalculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treecalculator.h; sourceTree = "<group>"; };
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 306                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = tree.cpp; sourceTree = "<group>"; };
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 308                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readtree.cpp; sourceTree = "<group>"; };
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 310                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = "<group>"; };
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 312                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
 313                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = "<group>"; };
 314                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = "<group>"; };
 315                 37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = "<group>"; };
 316                 37C753CD0FB3415200DBD02E /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = "<group>"; };
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 318                 37C753ED0FB34A5700DBD02E /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = "<group>"; };
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 320                 37C753F10FB34B4700DBD02E /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = "<group>"; };
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 322                 37C753F40FB34C0300DBD02E /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = "<group>"; };
 323                 37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
 324                 37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
 325                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = "<group>"; };
 326                 37D927BB0F21331F001D4494 /* bootstrap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bootstrap.cpp; sourceTree = "<group>"; };
 327                 37D927BC0F21331F001D4494 /* bootstrap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bootstrap.h; sourceTree = "<group>"; };
 328                 37D927BD0F21331F001D4494 /* calculator.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = calculator.cpp; sourceTree = "<group>"; };
 329                 37D927BE0F21331F001D4494 /* calculator.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = calculator.h; sourceTree = "<group>"; };
 330                 37D927BF0F21331F001D4494 /* chao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chao1.cpp; sourceTree = "<group>"; };
 331                 37D927C00F21331F001D4494 /* chao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chao1.h; sourceTree = "<group>"; };
 332                 37D927C10F21331F001D4494 /* cluster.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = cluster.cpp; sourceTree = "<group>"; };
 333                 37D927C20F21331F001D4494 /* cluster.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = cluster.hpp; sourceTree = "<group>"; };
 334                 37D927C30F21331F001D4494 /* clustercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustercommand.cpp; sourceTree = "<group>"; };
 335                 37D927C40F21331F001D4494 /* clustercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustercommand.h; sourceTree = "<group>"; };
 336                 37D927C50F21331F001D4494 /* collect.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collect.cpp; sourceTree = "<group>"; };
 337                 37D927C60F21331F001D4494 /* collect.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collect.h; sourceTree = "<group>"; };
 338                 37D927C70F21331F001D4494 /* collectcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectcommand.cpp; sourceTree = "<group>"; };
 339                 37D927C80F21331F001D4494 /* collectcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectcommand.h; sourceTree = "<group>"; };
 340                 37D927C90F21331F001D4494 /* collectdisplay.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectdisplay.h; sourceTree = "<group>"; };
 341                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectorscurvedata.h; sourceTree = "<group>"; };
 342                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = collectsharedcommand.cpp; sourceTree = "<group>"; };
 343                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = collectsharedcommand.h; sourceTree = "<group>"; };
 344                 37D927CD0F21331F001D4494 /* command.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = command.hpp; sourceTree = "<group>"; };
 345                 37D927CF0F21331F001D4494 /* commandfactory.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandfactory.hpp; sourceTree = "<group>"; };
 346                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = commandoptionparser.cpp; sourceTree = "<group>"; };
 347                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = commandoptionparser.hpp; sourceTree = "<group>"; };
 348                 37D927D20F21331F001D4494 /* completelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = completelinkage.cpp; sourceTree = "<group>"; };
 349                 37D927D30F21331F001D4494 /* database.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = database.cpp; sourceTree = "<group>"; };
 350                 37D927D40F21331F001D4494 /* database.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = database.hpp; sourceTree = "<group>"; };
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 353                 37D927D70F21331F001D4494 /* engine.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = engine.cpp; sourceTree = "<group>"; };
 354                 37D927D80F21331F001D4494 /* engine.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = engine.hpp; sourceTree = "<group>"; };
 355                 37D927D90F21331F001D4494 /* errorchecking.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = errorchecking.cpp; sourceTree = "<group>"; };
 356                 37D927DA0F21331F001D4494 /* errorchecking.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = errorchecking.h; sourceTree = "<group>"; };
 357                 37D927DB0F21331F001D4494 /* fastamap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fastamap.cpp; sourceTree = "<group>"; };
 358                 37D927DC0F21331F001D4494 /* fastamap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fastamap.h; sourceTree = "<group>"; };
 359                 37D927DD0F21331F001D4494 /* fileoutput.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fileoutput.cpp; sourceTree = "<group>"; };
 360                 37D927DE0F21331F001D4494 /* fileoutput.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fileoutput.h; sourceTree = "<group>"; };
 361                 37D927DF0F21331F001D4494 /* globaldata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = globaldata.cpp; sourceTree = "<group>"; };
 362                 37D927E00F21331F001D4494 /* globaldata.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = globaldata.hpp; sourceTree = "<group>"; };
 363                 37D927E10F21331F001D4494 /* groupmap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = groupmap.cpp; sourceTree = "<group>"; };
 364                 37D927E20F21331F001D4494 /* groupmap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = groupmap.h; sourceTree = "<group>"; };
 365                 37D927E30F21331F001D4494 /* helpcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = helpcommand.cpp; sourceTree = "<group>"; };
 366                 37D927E40F21331F001D4494 /* helpcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = helpcommand.h; sourceTree = "<group>"; };
 367                 37D927E50F21331F001D4494 /* inputdata.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = inputdata.cpp; sourceTree = "<group>"; };
 368                 37D927E60F21331F001D4494 /* inputdata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = inputdata.h; sourceTree = "<group>"; };
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 370                 37D927E80F21331F001D4494 /* jackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = jackknife.h; sourceTree = "<group>"; };
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 372                 37D927EA0F21331F001D4494 /* kmer.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = kmer.hpp; sourceTree = "<group>"; };
 373                 37D927EB0F21331F001D4494 /* kmerdb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = kmerdb.cpp; sourceTree = "<group>"; };
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 375                 37D927ED0F21331F001D4494 /* listvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listvector.cpp; sourceTree = "<group>"; };
 376                 37D927EE0F21331F001D4494 /* listvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = listvector.hpp; sourceTree = "<group>"; };
 377                 37D927EF0F21331F001D4494 /* mothur.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = mothur.cpp; sourceTree = "<group>"; };
 378                 37D927F00F21331F001D4494 /* nameassignment.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = nameassignment.cpp; sourceTree = "<group>"; };
 379                 37D927F10F21331F001D4494 /* nameassignment.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = nameassignment.hpp; sourceTree = "<group>"; };
 380                 37D927F40F21331F001D4494 /* npshannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = npshannon.cpp; sourceTree = "<group>"; };
 381                 37D927F50F21331F001D4494 /* npshannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = npshannon.h; sourceTree = "<group>"; };
 382                 37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = "<group>"; };
 383                 37D927F70F21331F001D4494 /* ordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ordervector.cpp; sourceTree = "<group>"; };
 384                 37D927F80F21331F001D4494 /* ordervector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = ordervector.hpp; sourceTree = "<group>"; };
 385                 37D927F90F21331F001D4494 /* parselistcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parselistcommand.cpp; sourceTree = "<group>"; };
 386                 37D927FA0F21331F001D4494 /* parselistcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parselistcommand.h; sourceTree = "<group>"; };
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 388                 37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = "<group>"; };
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 390                 37D927FE0F21331F001D4494 /* quitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = quitcommand.h; sourceTree = "<group>"; };
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 393                 37D928010F21331F001D4494 /* rarecalc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarecalc.cpp; sourceTree = "<group>"; };
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 395                 37D928030F21331F001D4494 /* raredisplay.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = raredisplay.cpp; sourceTree = "<group>"; };
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 398                 37D928060F21331F001D4494 /* rarefact.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefact.h; sourceTree = "<group>"; };
 399                 37D928070F21331F001D4494 /* rarefactcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactcommand.cpp; sourceTree = "<group>"; };
 400                 37D928080F21331F001D4494 /* rarefactcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactcommand.h; sourceTree = "<group>"; };
 401                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactioncurvedata.h; sourceTree = "<group>"; };
 402                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = rarefactsharedcommand.cpp; sourceTree = "<group>"; };
 403                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = rarefactsharedcommand.h; sourceTree = "<group>"; };
 404                 37D928130F21331F001D4494 /* readmatrix.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = readmatrix.hpp; sourceTree = "<group>"; };
 405                 37D9281A0F21331F001D4494 /* sabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sabundvector.cpp; sourceTree = "<group>"; };
 406                 37D9281B0F21331F001D4494 /* sabundvector.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sabundvector.hpp; sourceTree = "<group>"; };
 407                 37D9281C0F21331F001D4494 /* sequence.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequence.cpp; sourceTree = "<group>"; };
 408                 37D9281D0F21331F001D4494 /* sequence.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = sequence.hpp; sourceTree = "<group>"; };
 409                 37D9281E0F21331F001D4494 /* shannon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannon.cpp; sourceTree = "<group>"; };
 410                 37D9281F0F21331F001D4494 /* shannon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannon.h; sourceTree = "<group>"; };
 411                 37D928200F21331F001D4494 /* shared.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shared.cpp; sourceTree = "<group>"; };
 412                 37D928210F21331F001D4494 /* shared.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shared.h; sourceTree = "<group>"; };
 413                 37D928220F21331F001D4494 /* sharedace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedace.cpp; sourceTree = "<group>"; };
 414                 37D928230F21331F001D4494 /* sharedace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedace.h; sourceTree = "<group>"; };
 415                 37D928240F21331F001D4494 /* sharedchao1.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedchao1.cpp; sourceTree = "<group>"; };
 416                 37D928250F21331F001D4494 /* sharedchao1.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedchao1.h; sourceTree = "<group>"; };
 417                 37D928260F21331F001D4494 /* sharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedcommand.cpp; sourceTree = "<group>"; };
 418                 37D928270F21331F001D4494 /* sharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedcommand.h; sourceTree = "<group>"; };
 419                 37D928280F21331F001D4494 /* sharedjabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjabund.cpp; sourceTree = "<group>"; };
 420                 37D928290F21331F001D4494 /* sharedjabund.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjabund.h; sourceTree = "<group>"; };
 421                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjclass.cpp; sourceTree = "<group>"; };
 422                 37D9282B0F21331F001D4494 /* sharedjclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjclass.h; sourceTree = "<group>"; };
 423                 37D9282C0F21331F001D4494 /* sharedjest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjest.cpp; sourceTree = "<group>"; };
 424                 37D9282D0F21331F001D4494 /* sharedjest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjest.h; sourceTree = "<group>"; };
 425                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedordervector.cpp; sourceTree = "<group>"; };
 426                 37D9282F0F21331F001D4494 /* sharedordervector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedordervector.h; sourceTree = "<group>"; };
 427                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundvector.cpp; sourceTree = "<group>"; };
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 429                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsabundvector.cpp; sourceTree = "<group>"; };
 430                 37D928330F21331F001D4494 /* sharedsabundvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsabundvector.h; sourceTree = "<group>"; };
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 433                 37D928360F21331F001D4494 /* sharedsorabund.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorabund.cpp; sourceTree = "<group>"; };
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 435                 37D928380F21331F001D4494 /* sharedsorclass.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorclass.cpp; sourceTree = "<group>"; };
 436                 37D928390F21331F001D4494 /* sharedsorclass.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorclass.h; sourceTree = "<group>"; };
 437                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsorest.cpp; sourceTree = "<group>"; };
 438                 37D9283B0F21331F001D4494 /* sharedsorest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedsorest.h; sourceTree = "<group>"; };
 439                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetan.cpp; sourceTree = "<group>"; };
 440                 37D9283D0F21331F001D4494 /* sharedthetan.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetan.h; sourceTree = "<group>"; };
 441                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedthetayc.cpp; sourceTree = "<group>"; };
 442                 37D9283F0F21331F001D4494 /* sharedthetayc.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedthetayc.h; sourceTree = "<group>"; };
 443                 37D928400F21331F001D4494 /* simpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpson.cpp; sourceTree = "<group>"; };
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 453                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = summarysharedcommand.cpp; sourceTree = "<group>"; };
 454                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = summarysharedcommand.h; sourceTree = "<group>"; };
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 481                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupcommand.h; sourceTree = "<group>"; };
 482                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlabelcommand.cpp; sourceTree = "<group>"; };
 483                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlabelcommand.h; sourceTree = "<group>"; };
 484                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlinecommand.cpp; sourceTree = "<group>"; };
 485                 A70B53A90F4CD7AD0064797E /* getlinecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlinecommand.h; sourceTree = "<group>"; };
 486                 C6859E8B029090EE04C91782 /* Mothur.1 */ = {isa = PBXFileReference; lastKnownFileType = text.man; path = Mothur.1; sourceTree = "<group>"; };
 487                 EB1216860F619B83004A865F /* bergerparker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bergerparker.h; sourceTree = "<group>"; };
 488                 EB1216870F619B83004A865F /* bergerparker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bergerparker.cpp; sourceTree = "<group>"; };
 489                 EB1216E30F61ACFB004A865F /* bstick.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bstick.h; sourceTree = "<group>"; };
 490                 EB1216E40F61ACFB004A865F /* bstick.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bstick.cpp; sourceTree = "<group>"; };
 491                 EB1217210F61C9AC004A865F /* sharedkstest.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedkstest.h; sourceTree = "<group>"; };
 492                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = "<group>"; };
 493                 EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = "<group>"; };
 494                 EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = "<group>"; };
 495                 EB72FE240FC1F5CA0051AC11 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = "<group>"; };
 496                 EB72FE250FC1F5CA0051AC11 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = "<group>"; };
 497                 EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
 498                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
 499                 EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = "<group>"; };
 500                 EB9303F80F53517300E8EF26 /* geom.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = geom.cpp; sourceTree = "<group>"; };
 501 /* End PBXFileReference section */
 502
 503 /* Begin PBXFrameworksBuildPhase section */
 504                 8DD76F660486A84900D96B5E /* Frameworks */ = {
 505                         isa = PBXFrameworksBuildPhase;
 506                         buildActionMask = 2147483647;
 507                         files = (
 508                         );
 509                         runOnlyForDeploymentPostprocessing = 0;
 510                 };
 511 /* End PBXFrameworksBuildPhase section */
 512
 513 /* Begin PBXGroup section */
 514                 08FB7794FE84155DC02AAC07 /* Mothur */ = {
 515                         isa = PBXGroup;
 516                         children = (
 517                                 08FB7795FE84155DC02AAC07 /* Source */,
 518                                 C6859E8C029090F304C91782 /* Documentation */,
 519                                 1AB674ADFE9D54B511CA2CBB /* Products */,
 520                         );
 521                         name = Mothur;
 522                         sourceTree = "<group>";
 523                 };
 524                 08FB7795FE84155DC02AAC07 /* Source */ = {
 525                         isa = PBXGroup;
 526                         children = (
 527                                 37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
 528                                 373C68DC0FC1C38D00137ACD /* blastalign.hpp */,
 529                                 373C68DB0FC1C38D00137ACD /* blastalign.cpp */,
 530                                 37D928A60F2133C0001D4494 /* calculators */,
 531                                 37D927C20F21331F001D4494 /* cluster.hpp */,
 532                                 37D927C10F21331F001D4494 /* cluster.cpp */,
 533                                 37D928A90F2133E5001D4494 /* commands */,
 534                                 37D927C60F21331F001D4494 /* collect.h */,
 535                                 37D927C50F21331F001D4494 /* collect.cpp */,
 536                                 37D927C90F21331F001D4494 /* collectdisplay.h */,
 537                                 37D928AC0F213420001D4494 /* containers */,
 538                                 37D927CA0F21331F001D4494 /* collectorscurvedata.h */,
 539                                 37D927CF0F21331F001D4494 /* commandfactory.hpp */,
 540                                 372E12EC0F264D320095CF7E /* commandfactory.cpp */,
 541                                 37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
 542                                 37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
 543                                 37D927D20F21331F001D4494 /* completelinkage.cpp */,
 544                                 7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
 545                                 7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
 546                                 37D927D60F21331F001D4494 /* display.h */,
 547                                 37D927D80F21331F001D4494 /* engine.hpp */,
 548                                 37D927D70F21331F001D4494 /* engine.cpp */,
 549                                 37D928B10F213472001D4494 /* errorcheckor */,
 550                                 37D927DE0F21331F001D4494 /* fileoutput.h */,
 551                                 37D927DD0F21331F001D4494 /* fileoutput.cpp */,
 552                                 37D927E00F21331F001D4494 /* globaldata.hpp */,
 553                                 37D927DF0F21331F001D4494 /* globaldata.cpp */,
 554                                 373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */,
 555                                 373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
 556                                 375873ED0F7D646F0040F377 /* heatmap.h */,
 557                                 375873EE0F7D646F0040F377 /* heatmap.cpp */,
 558                                 37D927E60F21331F001D4494 /* inputdata.h */,
 559                                 37D927E50F21331F001D4494 /* inputdata.cpp */,
 560                                 7E412F420F8D213C00381DD0 /* libshuff.h */,
 561                                 7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
 562                                 37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
 563                                 37D927EF0F21331F001D4494 /* mothur.cpp */,
 564                                 37D927F10F21331F001D4494 /* nameassignment.hpp */,
 565                                 37D927F00F21331F001D4494 /* nameassignment.cpp */,
 566                                 373C691E0FC1C98600137ACD /* nast.hpp */,
 567                                 373C691D0FC1C98600137ACD /* nast.cpp */,
 568                                 373C692A0FC1C9EB00137ACD /* nastreport.hpp */,
 569                                 373C69290FC1C9EB00137ACD /* nastreport.cpp */,
 570                                 373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */,
 571                                 373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */,
 572                                 373C68E40FC1C4A500137ACD /* noalign.hpp */,
 573                                 373C68E30FC1C4A500137ACD /* noalign.cpp */,
 574                                 37D927F60F21331F001D4494 /* observable.h */,
 575                                 373C68C40FC1C25F00137ACD /* overlap.hpp */,
 576                                 373C68C30FC1C25F00137ACD /* overlap.cpp */,
 577                                 37D927FC0F21331F001D4494 /* progress.hpp */,
 578                                 37D927FB0F21331F001D4494 /* progress.cpp */,
 579                                 37D928040F21331F001D4494 /* raredisplay.h */,
 580                                 37D928030F21331F001D4494 /* raredisplay.cpp */,
 581                                 37D928060F21331F001D4494 /* rarefact.h */,
 582                                 37D928050F21331F001D4494 /* rarefact.cpp */,
 583                                 37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
 584                                 3796441D0FB9B9650081FDB6 /* read */,
 585                                 37D928210F21331F001D4494 /* shared.h */,
 586                                 37D928200F21331F001D4494 /* shared.cpp */,
 587                                 211C38310F961DD400FEE541 /* sharedutilities.h */,
 588                                 211C38300F961DD400FEE541 /* sharedutilities.cpp */,
 589                                 37D928420F21331F001D4494 /* singlelinkage.cpp */,
 590                                 7E412F470F8D21B600381DD0 /* slibshuff.h */,
 591                                 7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
 592                                 37D928480F21331F001D4494 /* summarydata.h */,
 593                                 37D928490F21331F001D4494 /* summarydisplay.h */,
 594                                 37519AB30F810FAE00FED5E8 /* venn.h */,
 595                                 37519AB40F810FAE00FED5E8 /* venn.cpp */,
 596                         );
 597                         name = Source;
 598                         sourceTree = "<group>";
 599                 };
 600                 1AB674ADFE9D54B511CA2CBB /* Products */ = {
 601                         isa = PBXGroup;
 602                         children = (
 603                                 8DD76F6C0486A84900D96B5E /* mothur */,
 604                         );
 605                         name = Products;
 606                         sourceTree = "<group>";
 607                 };
 608                 3796441D0FB9B9650081FDB6 /* read */ = {
 609                         isa = PBXGroup;
 610                         children = (
 611                                 378C1AF30FB0644D004D63F5 /* readclustal.h */,
 612                                 378C1AF20FB0644D004D63F5 /* readclustal.cpp */,
 613                                 375AA1340F9E433D008EF9B8 /* readcolumn.h */,
 614                                 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
 615                                 378C1AF50FB0644D004D63F5 /* readfasta.h */,
 616                                 378C1AF40FB0644D004D63F5 /* readfasta.cpp */,
 617                                 37D928130F21331F001D4494 /* readmatrix.hpp */,
 618                                 378C1AF70FB0644D004D63F5 /* readnexus.h */,
 619                                 378C1AF60FB0644D004D63F5 /* readnexus.cpp */,
 620                                 378C1AF80FB0644D004D63F5 /* readnexusal.h */,
 621                                 375AA1360F9E433D008EF9B8 /* readotu.h */,
 622                                 375AA1350F9E433D008EF9B8 /* readotu.cpp */,
 623                                 375AA1380F9E433D008EF9B8 /* readphylip.h */,
 624                                 375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
 625                                 378C1AFC0FB0644D004D63F5 /* readseqsphylip.h */,
 626                                 378C1AFB0FB0644D004D63F5 /* readseqsphylip.cpp */,
 627                                 379643EB0FB9B5A80081FDB6 /* readseqs.cpp */,
 628                                 379643EC0FB9B5A80081FDB6 /* readseqs.h */,
 629                                 37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
 630                                 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
 631                         );
 632                         name = read;
 633                         sourceTree = "<group>";
 634                 };
 635                 37D928A60F2133C0001D4494 /* calculators */ = {
 636                         isa = PBXGroup;
 637                         children = (
 638                                 37D927BE0F21331F001D4494 /* calculator.h */,
 639                                 373C69950FC1E63600137ACD /* boneh.h */,
 640                                 373C69940FC1E63600137ACD /* boneh.cpp */,
 641                                 3792948D0F2E271100B9034A /* treecalculator.h */,
 642                                 37D927BD0F21331F001D4494 /* calculator.cpp */,
 643                                 37D927B90F21331F001D4494 /* ace.h */,
 644                                 37D927B80F21331F001D4494 /* ace.cpp */,
 645                                 EB1216860F619B83004A865F /* bergerparker.h */,
 646                                 EB1216870F619B83004A865F /* bergerparker.cpp */,
 647                                 37D927BC0F21331F001D4494 /* bootstrap.h */,
 648                                 37D927BB0F21331F001D4494 /* bootstrap.cpp */,
 649                                 EB1216E30F61ACFB004A865F /* bstick.h */,
 650                                 EB1216E40F61ACFB004A865F /* bstick.cpp */,
 651                                 37D927C00F21331F001D4494 /* chao1.h */,
 652                                 37D927BF0F21331F001D4494 /* chao1.cpp */,
 653                                 7EC3D4510FA0FFF900338DA5 /* coverage.h */,
 654                                 7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
 655                                 37C753DF0FB3492400DBD02E /* dist.h */,
 656                                 37C753F00FB34AE800DBD02E /* eachgapdist.h */,
 657                                 37C753F40FB34C0300DBD02E /* eachgapignore.h */,
 658                                 373C69960FC1E63600137ACD /* efron.cpp */,
 659                                 373C69970FC1E63600137ACD /* efron.h */,
 660                                 EB9303F70F53517300E8EF26 /* geom.h */,
 661                                 EB9303F80F53517300E8EF26 /* geom.cpp */,
 662                                 378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
 663                                 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */,
 664                                 37C753ED0FB34A5700DBD02E /* ignoregaps.h */,
 665                                 37D927E80F21331F001D4494 /* jackknife.h */,
 666                                 37D927E70F21331F001D4494 /* jackknife.cpp */,
 667                                 EB9303E90F534D9400E8EF26 /* logsd.h */,
 668                                 EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
 669                                 375873F90F7D64AB0040F377 /* nseqs.h */,
 670                                 37D927F50F21331F001D4494 /* npshannon.h */,
 671                                 37D927F40F21331F001D4494 /* npshannon.cpp */,
 672                                 37C753F10FB34B4700DBD02E /* onegapdist.h */,
 673                                 37C753F30FB34BBF00DBD02E /* onegapignore.h */,
 674                                 379294880F2E258500B9034A /* parsimony.h */,
 675                                 379294890F2E258500B9034A /* parsimony.cpp */,
 676                                 EB6E68170F5F1C780044E17B /* qstat.h */,
 677                                 EB6E68180F5F1C780044E17B /* qstat.cpp */,
 678                                 37D928020F21331F001D4494 /* rarecalc.h */,
 679                                 37D928010F21331F001D4494 /* rarecalc.cpp */,
 680                                 37D9281F0F21331F001D4494 /* shannon.h */,
 681                                 37D9281E0F21331F001D4494 /* shannon.cpp */,
 682                                 37D928230F21331F001D4494 /* sharedace.h */,
 683                                 37D928220F21331F001D4494 /* sharedace.cpp */,
 684                                 37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
 685                                 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
 686                                 7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
 687                                 375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
 688                                 375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
 689                                 37D928250F21331F001D4494 /* sharedchao1.h */,
 690                                 37D928240F21331F001D4494 /* sharedchao1.cpp */,
 691                                 37D928290F21331F001D4494 /* sharedjabund.h */,
 692                                 37D928280F21331F001D4494 /* sharedjabund.cpp */,
 693                                 378C1B000FB0644D004D63F5 /* sharedjackknife.h */,
 694                                 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */,
 695                                 37D9282B0F21331F001D4494 /* sharedjclass.h */,
 696                                 37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
 697                                 37D9282D0F21331F001D4494 /* sharedjest.h */,
 698                                 37D9282C0F21331F001D4494 /* sharedjest.cpp */,
 699                                 EB1217210F61C9AC004A865F /* sharedkstest.h */,
 700                                 EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
 701                                 375874000F7D64EF0040F377 /* sharedkulczynski.h */,
 702                                 375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
 703                                 375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
 704                                 375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
 705                                 375874010F7D64EF0040F377 /* sharedlennon.h */,
 706                                 375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
 707                                 378C1B020FB0644D004D63F5 /* sharedmarczewski.h */,
 708                                 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */,
 709                                 375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
 710                                 375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
 711                                 375874090F7D64FC0040F377 /* sharedochiai.h */,
 712                                 3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
 713                                 3758740A0F7D64FC0040F377 /* sharednseqs.h */,
 714                                 37D928350F21331F001D4494 /* sharedsobs.h */,
 715                                 37D928340F21331F001D4494 /* sharedsobs.cpp */,
 716                                 37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
 717                                 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
 718                                 37D928370F21331F001D4494 /* sharedsorabund.h */,
 719                                 37D928360F21331F001D4494 /* sharedsorabund.cpp */,
 720                                 37D928390F21331F001D4494 /* sharedsorclass.h */,
 721                                 37D928380F21331F001D4494 /* sharedsorclass.cpp */,
 722                                 37D9283B0F21331F001D4494 /* sharedsorest.h */,
 723                                 37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
 724                                 37D9283D0F21331F001D4494 /* sharedthetan.h */,
 725                                 37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
 726                                 37D9283F0F21331F001D4494 /* sharedthetayc.h */,
 727                                 37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
 728                                 EB72FE250FC1F5CA0051AC11 /* shen.h */,
 729                                 EB72FE240FC1F5CA0051AC11 /* shen.cpp */,
 730                                 37D928410F21331F001D4494 /* simpson.h */,
 731                                 37D928400F21331F001D4494 /* simpson.cpp */,
 732                                 37D928430F21331F001D4494 /* sobs.h */,
 733                                 373C69980FC1E63600137ACD /* solow.cpp */,
 734                                 373C69990FC1E63600137ACD /* solow.h */,
 735                                 374610810F40652400460C57 /* unweighted.h */,
 736                                 374610820F40652400460C57 /* unweighted.cpp */,
 737                                 37D9284E0F21331F001D4494 /* uvest.h */,
 738                                 37D9284D0F21331F001D4494 /* uvest.cpp */,
 739                                 3746107C0F4064D100460C57 /* weighted.h */,
 740                                 3746107D0F4064D100460C57 /* weighted.cpp */,
 741                                 7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
 742                                 7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
 743                         );
 744                         name = calculators;
 745                         sourceTree = "<group>";
 746                 };
 747                 37D928A90F2133E5001D4494 /* commands */ = {
 748                         isa = PBXGroup;
 749                         children = (
 750                                 37D927CD0F21331F001D4494 /* command.hpp */,
 751                                 378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
 752                                 378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
 753                                 37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
 754                                 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
 755                                 21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
 756                                 21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
 757                                 37D927C40F21331F001D4494 /* clustercommand.h */,
 758                                 37D927C30F21331F001D4494 /* clustercommand.cpp */,
 759                                 37D927C80F21331F001D4494 /* collectcommand.h */,
 760                                 37D927C70F21331F001D4494 /* collectcommand.cpp */,
 761                                 37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
 762                                 37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
 763                                 377326640FAF16E0007ABB8B /* concensuscommand.h */,
 764                                 377326630FAF16E0007ABB8B /* concensuscommand.cpp */,
 765                                 37B28F660F27590100808A62 /* deconvolutecommand.h */,
 766                                 37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
 767                                 37C753CC0FB3415200DBD02E /* distancecommand.h */,
 768                                 37C753CD0FB3415200DBD02E /* distancecommand.cpp */,
 769                                 378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */,
 770                                 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */,
 771                                 A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
 772                                 A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
 773                                 A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
 774                                 A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
 775                                 A70B53A90F4CD7AD0064797E /* getlinecommand.h */,
 776                                 A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
 777                                 370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
 778                                 370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
 779                                 211A24E90FC306BC00769A33 /* getrepseqscommand.h */,
 780                                 211A24EA0FC306BC00769A33 /* getrepseqscommand.cpp */,
 781                                 375873F10F7D64800040F377 /* heatmapcommand.h */,
 782                                 375873F00F7D64800040F377 /* heatmapcommand.cpp */,
 783                                 37D927E40F21331F001D4494 /* helpcommand.h */,
 784                                 37D927E30F21331F001D4494 /* helpcommand.cpp */,
 785                                 375873F40F7D648F0040F377 /* libshuffcommand.h */,
 786                                 375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
 787                                 21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
 788                                 21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
 789                                 375873F60F7D649C0040F377 /* nocommands.cpp */,
 790                                 375873F70F7D649C0040F377 /* nocommands.h */,
 791                                 37D927FA0F21331F001D4494 /* parselistcommand.h */,
 792                                 37D927F90F21331F001D4494 /* parselistcommand.cpp */,
 793                                 3792946E0F2E191800B9034A /* parsimonycommand.h */,
 794                                 3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
 795                                 37D927FE0F21331F001D4494 /* quitcommand.h */,
 796                                 37D927FD0F21331F001D4494 /* quitcommand.cpp */,
 797                                 37D928080F21331F001D4494 /* rarefactcommand.h */,
 798                                 37D928070F21331F001D4494 /* rarefactcommand.cpp */,
 799                                 37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
 800                                 37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
 801                                 372E12940F263D5A0095CF7E /* readdistcommand.h */,
 802                                 372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
 803                                 372E126E0F26365B0095CF7E /* readotucommand.h */,
 804                                 372E126F0F26365B0095CF7E /* readotucommand.cpp */,
 805                                 37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
 806                                 37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
 807                                 37D928270F21331F001D4494 /* sharedcommand.h */,
 808                                 37D928260F21331F001D4494 /* sharedcommand.cpp */,
 809                                 37D928470F21331F001D4494 /* summarycommand.h */,
 810                                 37D928460F21331F001D4494 /* summarycommand.cpp */,
 811                                 37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
 812                                 37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
 813                                 211C38370F961E1F00FEE541 /* treegroupscommand.h */,
 814                                 211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
 815                                 3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
 816                                 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
 817                                 374610760F40645300460C57 /* unifracweightedcommand.h */,
 818                                 374610770F40645300460C57 /* unifracweightedcommand.cpp */,
 819                                 37519A9F0F810D0200FED5E8 /* venncommand.h */,
 820                                 37519AA00F810D0200FED5E8 /* venncommand.cpp */,
 821                         );
 822                         name = commands;
 823                         sourceTree = "<group>";
 824                 };
 825                 37D928AC0F213420001D4494 /* containers */ = {
 826                         isa = PBXGroup;
 827                         children = (
 828                                 373C68A10FC1C07D00137ACD /* alignment.hpp */,
 829                                 373C68A00FC1C07D00137ACD /* alignment.cpp */,
 830                                 373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
 831                                 373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
 832                                 373C69170FC1C8AF00137ACD /* blastdb.hpp */,
 833                                 373C69160FC1C8AF00137ACD /* blastdb.cpp */,
 834                                 37D927D40F21331F001D4494 /* database.hpp */,
 835                                 37D927D30F21331F001D4494 /* database.cpp */,
 836                                 37D927D50F21331F001D4494 /* datavector.hpp */,
 837                                 37D927DC0F21331F001D4494 /* fastamap.h */,
 838                                 37D927DB0F21331F001D4494 /* fastamap.cpp */,
 839                                 375873EA0F7D64520040F377 /* fullmatrix.h */,
 840                                 375873EB0F7D64520040F377 /* fullmatrix.cpp */,
 841                                 37D927E20F21331F001D4494 /* groupmap.h */,
 842                                 37D927E10F21331F001D4494 /* groupmap.cpp */,
 843                                 37D927EA0F21331F001D4494 /* kmer.hpp */,
 844                                 37D927E90F21331F001D4494 /* kmer.cpp */,
 845                                 37D927EC0F21331F001D4494 /* kmerdb.hpp */,
 846                                 37D927EB0F21331F001D4494 /* kmerdb.cpp */,
 847                                 37D927EE0F21331F001D4494 /* listvector.hpp */,
 848                                 37D927ED0F21331F001D4494 /* listvector.cpp */,
 849                                 37D927F80F21331F001D4494 /* ordervector.hpp */,
 850                                 37D927F70F21331F001D4494 /* ordervector.cpp */,
 851                                 37D928000F21331F001D4494 /* rabundvector.hpp */,
 852                                 37D927FF0F21331F001D4494 /* rabundvector.cpp */,
 853                                 37D9281B0F21331F001D4494 /* sabundvector.hpp */,
 854                                 37D9281A0F21331F001D4494 /* sabundvector.cpp */,
 855                                 37D9281D0F21331F001D4494 /* sequence.hpp */,
 856                                 37D9281C0F21331F001D4494 /* sequence.cpp */,
 857                                 378C1AFE0FB0644D004D63F5 /* sequencedb.h */,
 858                                 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */,
 859                                 37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
 860                                 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
 861                                 37D9282F0F21331F001D4494 /* sharedordervector.h */,
 862                                 37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
 863                                 37D928310F21331F001D4494 /* sharedrabundvector.h */,
 864                                 37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
 865                                 37D928330F21331F001D4494 /* sharedsabundvector.h */,
 866                                 37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
 867                                 37D928450F21331F001D4494 /* sparsematrix.hpp */,
 868                                 37D928440F21331F001D4494 /* sparsematrix.cpp */,
 869                                 373C68F40FC1C6A800137ACD /* suffixdb.hpp */,
 870                                 373C68F30FC1C6A800137ACD /* suffixdb.cpp */,
 871                                 373C68F60FC1C6A800137ACD /* suffixnodes.hpp */,
 872                                 373C68F50FC1C6A800137ACD /* suffixnodes.cpp */,
 873                                 373C68F80FC1C6A800137ACD /* suffixtree.hpp */,
 874                                 373C68F70FC1C6A800137ACD /* suffixtree.cpp */,
 875                                 37AD4DB90F28E2FE00AA2D49 /* tree.h */,
 876                                 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
 877                                 379293C10F2DE73400B9034A /* treemap.h */,
 878                                 379293C20F2DE73400B9034A /* treemap.cpp */,
 879                                 37E5F3E10F29FD4200F8D827 /* treenode.h */,
 880                                 37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
 881                         );
 882                         name = containers;
 883                         sourceTree = "<group>";
 884                 };
 885                 37D928B10F213472001D4494 /* errorcheckor */ = {
 886                         isa = PBXGroup;
 887                         children = (
 888                                 37D927DA0F21331F001D4494 /* errorchecking.h */,
 889                                 37D927D90F21331F001D4494 /* errorchecking.cpp */,
 890                                 37D928500F21331F001D4494 /* validcalculator.h */,
 891                                 37D9284F0F21331F001D4494 /* validcalculator.cpp */,
 892                                 37D928520F21331F001D4494 /* validcommands.h */,
 893                                 37D928510F21331F001D4494 /* validcommands.cpp */,
 894                                 37D928540F21331F001D4494 /* validparameter.h */,
 895                                 37D928530F21331F001D4494 /* validparameter.cpp */,
 896                         );
 897                         name = errorcheckor;
 898                         sourceTree = "<group>";
 899                 };
 900                 C6859E8C029090F304C91782 /* Documentation */ = {
 901                         isa = PBXGroup;
 902                         children = (
 903                                 C6859E8B029090EE04C91782 /* Mothur.1 */,
 904                         );
 905                         name = Documentation;
 906                         sourceTree = "<group>";
 907                 };
 908 /* End PBXGroup section */
 909
 910 /* Begin PBXNativeTarget section */
 911                 8DD76F620486A84900D96B5E /* mothur */ = {
 912                         isa = PBXNativeTarget;
 913                         buildConfigurationList = 1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */;
 914                         buildPhases = (
 915                                 8DD76F640486A84900D96B5E /* Sources */,
 916                                 8DD76F660486A84900D96B5E /* Frameworks */,
 917                                 8DD76F690486A84900D96B5E /* CopyFiles */,
 918                         );
 919                         buildRules = (
 920                         );
 921                         dependencies = (
 922                         );
 923                         name = mothur;
 924                         productInstallPath = "$(HOME)/bin";
 925                         productName = Mothur;
 926                         productReference = 8DD76F6C0486A84900D96B5E /* mothur */;
 927                         productType = "com.apple.product-type.tool";
 928                 };
 929 /* End PBXNativeTarget section */
 930
 931 /* Begin PBXProject section */
 932                 08FB7793FE84155DC02AAC07 /* Project object */ = {
 933                         isa = PBXProject;
 934                         buildConfigurationList = 1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */;
 935                         compatibilityVersion = "Xcode 3.0";
 936                         hasScannedForEncodings = 1;
 937                         mainGroup = 08FB7794FE84155DC02AAC07 /* Mothur */;
 938                         projectDirPath = "";
 939                         projectRoot = "";
 940                         targets = (
 941                                 8DD76F620486A84900D96B5E /* mothur */,
 942                         );
 943                 };
 944 /* End PBXProject section */
 945
 946 /* Begin PBXSourcesBuildPhase section */
 947                 8DD76F640486A84900D96B5E /* Sources */ = {
 948                         isa = PBXSourcesBuildPhase;
 949                         buildActionMask = 2147483647;
 950                         files = (
 951                                 37D928550F21331F001D4494 /* ace.cpp in Sources */,
 952                                 37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */,
 953                                 37D928570F21331F001D4494 /* bootstrap.cpp in Sources */,
 954                                 37D928580F21331F001D4494 /* calculator.cpp in Sources */,
 955                                 37D928590F21331F001D4494 /* chao1.cpp in Sources */,
 956                                 37D9285A0F21331F001D4494 /* cluster.cpp in Sources */,
 957                                 37D9285B0F21331F001D4494 /* clustercommand.cpp in Sources */,
 958                                 37D9285C0F21331F001D4494 /* collect.cpp in Sources */,
 959                                 37D9285D0F21331F001D4494 /* collectcommand.cpp in Sources */,
 960                                 37D9285E0F21331F001D4494 /* collectsharedcommand.cpp in Sources */,
 961                                 37D928600F21331F001D4494 /* commandoptionparser.cpp in Sources */,
 962                                 37D928610F21331F001D4494 /* completelinkage.cpp in Sources */,
 963                                 37D928620F21331F001D4494 /* database.cpp in Sources */,
 964                                 37D928630F21331F001D4494 /* engine.cpp in Sources */,
 965                                 37D928640F21331F001D4494 /* errorchecking.cpp in Sources */,
 966                                 37D928650F21331F001D4494 /* fastamap.cpp in Sources */,
 967                                 37D928660F21331F001D4494 /* fileoutput.cpp in Sources */,
 968                                 37D928670F21331F001D4494 /* globaldata.cpp in Sources */,
 969                                 37D928680F21331F001D4494 /* groupmap.cpp in Sources */,
 970                                 37D928690F21331F001D4494 /* helpcommand.cpp in Sources */,
 971                                 37D9286A0F21331F001D4494 /* inputdata.cpp in Sources */,
 972                                 37D9286B0F21331F001D4494 /* jackknife.cpp in Sources */,
 973                                 37D9286C0F21331F001D4494 /* kmer.cpp in Sources */,
 974                                 37D9286D0F21331F001D4494 /* kmerdb.cpp in Sources */,
 975                                 37D9286E0F21331F001D4494 /* listvector.cpp in Sources */,
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1000                                 37D9288F0F21331F001D4494 /* sharedrabundvector.cpp in Sources */,
1001                                 37D928900F21331F001D4494 /* sharedsabundvector.cpp in Sources */,
1002                                 37D928910F21331F001D4494 /* sharedsobs.cpp in Sources */,
1003                                 37D928920F21331F001D4494 /* sharedsorabund.cpp in Sources */,
1004                                 37D928930F21331F001D4494 /* sharedsorclass.cpp in Sources */,
1005                                 37D928940F21331F001D4494 /* sharedsorest.cpp in Sources */,
1006                                 37D928950F21331F001D4494 /* sharedthetan.cpp in Sources */,
1007                                 37D928960F21331F001D4494 /* sharedthetayc.cpp in Sources */,
1008                                 37D928970F21331F001D4494 /* simpson.cpp in Sources */,
1009                                 37D928980F21331F001D4494 /* singlelinkage.cpp in Sources */,
1010                                 37D928990F21331F001D4494 /* sparsematrix.cpp in Sources */,
1011                                 37D9289A0F21331F001D4494 /* summarycommand.cpp in Sources */,
1012                                 37D9289B0F21331F001D4494 /* summarysharedcommand.cpp in Sources */,
1013                                 37D9289C0F21331F001D4494 /* uvest.cpp in Sources */,
1014                                 37D9289D0F21331F001D4494 /* validcalculator.cpp in Sources */,
1015                                 37D9289E0F21331F001D4494 /* validcommands.cpp in Sources */,
1016                                 37D9289F0F21331F001D4494 /* validparameter.cpp in Sources */,
1017                                 372E12700F26365B0095CF7E /* readotucommand.cpp in Sources */,
1018                                 372E12960F263D5A0095CF7E /* readdistcommand.cpp in Sources */,
1019                                 372E12ED0F264D320095CF7E /* commandfactory.cpp in Sources */,
1020                                 37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */,
1021                                 37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */,
1022                                 37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */,
1023                                 37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */,
1024                                 37E5F3E30F29FD4200F8D827 /* treenode.cpp in Sources */,
1025                                 37E5F4920F2A3DA800F8D827 /* readtreecommand.cpp in Sources */,
1026                                 379293C30F2DE73400B9034A /* treemap.cpp in Sources */,
1027                                 379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */,
1028                                 3792948A0F2E258500B9034A /* parsimony.cpp in Sources */,
1029                                 374610780F40645300460C57 /* unifracweightedcommand.cpp in Sources */,
1030                                 3746107E0F4064D100460C57 /* weighted.cpp in Sources */,
1031                                 374610830F40652400460C57 /* unweighted.cpp in Sources */,
1032                                 3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */,
1033                                 37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */,
1034                                 A70B53AA0F4CD7AD0064797E /* getgroupcommand.cpp in Sources */,
1035                                 A70B53AB0F4CD7AD0064797E /* getlabelcommand.cpp in Sources */,
1036                                 A70B53AC0F4CD7AD0064797E /* getlinecommand.cpp in Sources */,
1037                                 EB9303EB0F534D9400E8EF26 /* logsd.cpp in Sources */,
1038                                 EB9303F90F53517300E8EF26 /* geom.cpp in Sources */,
1039                                 EB6E68190F5F1C780044E17B /* qstat.cpp in Sources */,
1040                                 EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
1041                                 EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
1042                                 EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
1043                                 375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
1044                                 375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
1045                                 375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */,
1046                                 375873F50F7D648F0040F377 /* libshuffcommand.cpp in Sources */,
1047                                 375873F80F7D649C0040F377 /* nocommands.cpp in Sources */,
1048                                 375873FD0F7D64DA0040F377 /* sharedbraycurtis.cpp in Sources */,
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1050                                 375874050F7D64EF0040F377 /* sharedlennon.cpp in Sources */,
1051                                 375874060F7D64EF0040F377 /* sharedkulczynskicody.cpp in Sources */,
1052                                 3758740C0F7D64FC0040F377 /* sharedmorisitahorn.cpp in Sources */,
1053                                 3758740D0F7D64FC0040F377 /* sharedochiai.cpp in Sources */,
1054                                 37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */,
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1057                                 37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */,
1058                                 370B88070F8A4EE4005AB382 /* getoturepcommand.cpp in Sources */,
1059                                 7E412F490F8D21B600381DD0 /* slibshuff.cpp in Sources */,
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1063                                 211C38380F961E1F00FEE541 /* treegroupscommand.cpp in Sources */,
1064                                 21DDC01B0F97A8FE0060691C /* bootstrapsharedcommand.cpp in Sources */,
1065                                 375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */,
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1067                                 375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
1068                                 7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */,
1069                                 7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */,
1070                                 377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */,
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1072                                 378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */,
1073                                 378C1B050FB0644E004D63F5 /* readclustal.cpp in Sources */,
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1076                                 378C1B090FB0644E004D63F5 /* readseqsphylip.cpp in Sources */,
1077                                 378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */,
1078                                 378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */,
1079                                 378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */,
1080                                 37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */,
1081                                 379643ED0FB9B5A80081FDB6 /* readseqs.cpp in Sources */,
1082                                 378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */,
1083                                 373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */,
1084                                 373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */,
1085                                 373C68BC0FC1C1A600137ACD /* gotohoverlap.cpp in Sources */,
1086                                 373C68C50FC1C25F00137ACD /* overlap.cpp in Sources */,
1087                                 373C68CF0FC1C2D900137ACD /* needlemanoverlap.cpp in Sources */,
1088                                 373C68DD0FC1C38D00137ACD /* blastalign.cpp in Sources */,
1089                                 373C68E50FC1C4A500137ACD /* noalign.cpp in Sources */,
1090                                 373C68F90FC1C6A800137ACD /* suffixdb.cpp in Sources */,
1091                                 373C68FA0FC1C6A800137ACD /* suffixnodes.cpp in Sources */,
1092                                 373C68FB0FC1C6A800137ACD /* suffixtree.cpp in Sources */,
1093                                 373C69180FC1C8AF00137ACD /* blastdb.cpp in Sources */,
1094                                 373C691F0FC1C98600137ACD /* nast.cpp in Sources */,
1095                                 373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */,
1096                                 373C699A0FC1E63600137ACD /* boneh.cpp in Sources */,
1097                                 373C699B0FC1E63600137ACD /* efron.cpp in Sources */,
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1099                                 EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */,
1100                                 211A24EB0FC306BC00769A33 /* getrepseqscommand.cpp in Sources */,
1101                                 21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */,
1102                         );
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