X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=bdcb7e66f32312e94e949c5d660b3d6de48cf2b5;hb=1b4aa03040e61f4c2d47ce32cb12726dcdadb917;hp=2b7d8787c72c15eff10a16e7df12031de5a915c5;hpb=cfe70bbc94980a0177af465d3464db754673bd56;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 2b7d878..bdcb7e6 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,16 +7,44 @@
 	objects = {
 
 /* Begin PBXFileReference section */
+		7E4EBD43122018FB00D85E7B /* simpsoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = simpsoneven.h; sourceTree = "<group>"; };
+		7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = simpsoneven.cpp; sourceTree = "<group>"; };
+		7E5B28DC121FEFCC0005339C /* shannoneven.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shannoneven.h; sourceTree = "<group>"; };
+		7E5B28DD121FEFCC0005339C /* shannoneven.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shannoneven.cpp; sourceTree = "<group>"; };
+		7E5B2917121FF53C0005339C /* heip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heip.h; sourceTree = "<group>"; };
+		7E5B2918121FF53C0005339C /* heip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heip.cpp; sourceTree = "<group>"; };
+		7E5B294A121FFADC0005339C /* smithwilson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = smithwilson.h; sourceTree = "<group>"; };
+		7E5B294B121FFADC0005339C /* smithwilson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = smithwilson.cpp; sourceTree = "<group>"; };
+		7E84528511EF4BEB00564975 /* seqerrorcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqerrorcommand.h; sourceTree = "<group>"; };
+		7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqerrorcommand.cpp; sourceTree = "<group>"; };
+		7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qualityscores.h; sourceTree = "<group>"; };
+		7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qualityscores.cpp; sourceTree = "<group>"; };
+		7E962A40121F76B1007464B5 /* invsimpson.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = invsimpson.h; sourceTree = "<group>"; };
+		7E962A41121F76B1007464B5 /* invsimpson.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = invsimpson.cpp; sourceTree = "<group>"; };
+		7EA299BA11E384940022D8D3 /* sensspeccommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sensspeccommand.h; sourceTree = "<group>"; };
+		7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sensspeccommand.cpp; sourceTree = "<group>"; };
+		7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = weightedlinkage.cpp; sourceTree = "<group>"; };
 		A703FE931194645F002C397E /* makegroupcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = makegroupcommand.h; sourceTree = SOURCE_ROOT; };
 		A703FE941194645F002C397E /* makegroupcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = makegroupcommand.cpp; sourceTree = SOURCE_ROOT; };
+		A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = degapseqscommand.h; sourceTree = "<group>"; };
+		A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = degapseqscommand.cpp; sourceTree = "<group>"; };
+		A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrelabundcommand.h; sourceTree = "<group>"; };
+		A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrelabundcommand.cpp; sourceTree = "<group>"; };
+		A71BA75F1225694E00C57506 /* clearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcut.cpp; sourceTree = "<group>"; };
+		A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clustersplitcommand.cpp; sourceTree = "<group>"; };
+		A71D924311AEB42400D00CBC /* clustersplitcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clustersplitcommand.h; sourceTree = "<group>"; };
+		A71D924411AEB42400D00CBC /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = "<group>"; };
+		A71D924511AEB42400D00CBC /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = "<group>"; };
+		A71D924611AEB42400D00CBC /* splitmatrix.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitmatrix.cpp; sourceTree = "<group>"; };
+		A71D924711AEB42400D00CBC /* splitmatrix.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitmatrix.h; sourceTree = "<group>"; };
 		A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversitycommand.h; sourceTree = "<group>"; };
 		A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversitycommand.cpp; sourceTree = "<group>"; };
 		A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylodiversity.h; sourceTree = "<group>"; };
 		A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylodiversity.cpp; sourceTree = "<group>"; };
+		A732505E11E49EF100484B90 /* sffinfocommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sffinfocommand.h; sourceTree = "<group>"; };
+		A732505F11E49EF100484B90 /* sffinfocommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sffinfocommand.cpp; sourceTree = "<group>"; };
 		A73953DA11987ED100B0B160 /* chopseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chopseqscommand.h; sourceTree = "<group>"; };
 		A73953DB11987ED100B0B160 /* chopseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chopseqscommand.cpp; sourceTree = "<group>"; };
-		A73F163411A1951D0087CA57 /* splitabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = splitabundcommand.h; sourceTree = "<group>"; };
-		A73F163511A1951D0087CA57 /* splitabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitabundcommand.cpp; sourceTree = "<group>"; };
 		A747E79B1163442A00FB9042 /* chimeracheckcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeracheckcommand.h; sourceTree = "<group>"; };
 		A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeracheckcommand.cpp; sourceTree = "<group>"; };
 		A747E81C116365E000FB9042 /* chimeraslayercommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraslayercommand.h; sourceTree = "<group>"; };
@@ -26,12 +54,17 @@
 		A76AAD03117F322B003D8DA1 /* phylosummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = phylosummary.cpp; sourceTree = "<group>"; };
 		A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; };
 		A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = setlogfilecommand.cpp; sourceTree = SOURCE_ROOT; };
+		A780E6CB11E7745D00BB5718 /* endiannessmacros.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = endiannessmacros.h; sourceTree = "<group>"; };
 		A78254461164D7790002E2DD /* chimerapintailcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerapintailcommand.h; sourceTree = "<group>"; };
 		A78254471164D7790002E2DD /* chimerapintailcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerapintailcommand.cpp; sourceTree = "<group>"; };
 		A7825502116519F70002E2DD /* chimerabellerophoncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimerabellerophoncommand.h; sourceTree = "<group>"; };
 		A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimerabellerophoncommand.cpp; sourceTree = "<group>"; };
 		A78434881162224F00100BE0 /* chimeraccodecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraccodecommand.h; sourceTree = "<group>"; };
 		A78434891162224F00100BE0 /* chimeraccodecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraccodecommand.cpp; sourceTree = "<group>"; };
+		A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
+		A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedrabundfloatvector.cpp; sourceTree = "<group>"; };
+		A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = classifyotucommand.h; sourceTree = "<group>"; };
+		A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = classifyotucommand.cpp; sourceTree = "<group>"; };
 		A7D215C811996C6E00F13F13 /* clearcutcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcutcommand.h; sourceTree = "<group>"; };
 		A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clearcutcommand.cpp; sourceTree = "<group>"; };
 		A7D216061199C47F00F13F13 /* catchallcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = catchallcommand.h; sourceTree = "<group>"; };
@@ -434,6 +467,21 @@
 		A7DA217A113FECD400BF472F /* weighted.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = weighted.h; sourceTree = "<group>"; };
 		A7DA217B113FECD400BF472F /* whittaker.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = whittaker.cpp; sourceTree = "<group>"; };
 		A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
+		A7DF0AD4121EBB14004A03EA /* clearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clearcut.h; sourceTree = "<group>"; };
+		A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */ = {isa = PBXFileReference; explicitFileType = sourcecode.cpp.cpp; fileEncoding = 4; path = cmdargs.cpp; sourceTree = "<group>"; };
+		A7DF0AD6121EBB14004A03EA /* cmdargs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = cmdargs.h; sourceTree = "<group>"; };
+		A7DF0AD7121EBB14004A03EA /* common.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = common.h; sourceTree = "<group>"; };
+		A7DF0AD8121EBB14004A03EA /* dayhoff.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dayhoff.h; sourceTree = "<group>"; };
+		A7DF0AD9121EBB14004A03EA /* distclearcut.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distclearcut.cpp; sourceTree = "<group>"; };
+		A7DF0ADA121EBB14004A03EA /* distclearcut.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distclearcut.h; sourceTree = "<group>"; };
+		A7DF0ADB121EBB14004A03EA /* dmat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = dmat.cpp; sourceTree = "<group>"; };
+		A7DF0ADC121EBB14004A03EA /* dmat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dmat.h; sourceTree = "<group>"; };
+		A7DF0ADD121EBB14004A03EA /* fasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = fasta.cpp; sourceTree = "<group>"; };
+		A7DF0ADE121EBB14004A03EA /* fasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = fasta.h; sourceTree = "<group>"; };
+		A7DF0ADF121EBB14004A03EA /* getopt_long.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getopt_long.cpp; sourceTree = "<group>"; };
+		A7DF0AE0121EBB14004A03EA /* getopt_long.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getopt_long.h; sourceTree = "<group>"; };
+		A7DF0AE1121EBB14004A03EA /* prng.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = prng.cpp; sourceTree = "<group>"; };
+		A7DF0AE2121EBB14004A03EA /* prng.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = prng.h; sourceTree = "<group>"; };
 		A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsesffcommand.cpp; sourceTree = "<group>"; };
 		A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = "<group>"; };
 /* End PBXFileReference section */
@@ -453,6 +501,7 @@
 				A7CB593B11402EF90010EB83 /* calculators */,
 				A7CB594A11402FB40010EB83 /* chimeras */,
 				A7CB594511402F6E0010EB83 /* classifers */,
+				A7DF0AE5121EBC26004A03EA /* clearcutsource */,
 				A7CB593E11402F110010EB83 /* commands */,
 				A7CB594211402F430010EB83 /* containers */,
 				A7DA2023113FECD400BF472F /* collect.cpp */,
@@ -467,6 +516,7 @@
 				A7DA203C113FECD400BF472F /* display.h */,
 				A7DA2042113FECD400BF472F /* dlibshuff.cpp */,
 				A7DA2043113FECD400BF472F /* dlibshuff.h */,
+				A780E6CB11E7745D00BB5718 /* endiannessmacros.h */,
 				A7DA2048113FECD400BF472F /* engine.cpp */,
 				A7DA2049113FECD400BF472F /* engine.hpp */,
 				A7DA204C113FECD400BF472F /* fileoutput.cpp */,
@@ -556,7 +606,11 @@
 				A7DA2059113FECD400BF472F /* geom.h */,
 				A7DA206C113FECD400BF472F /* goodscoverage.cpp */,
 				A7DA206D113FECD400BF472F /* goodscoverage.h */,
+				7E5B2917121FF53C0005339C /* heip.h */,
+				7E5B2918121FF53C0005339C /* heip.cpp */,
 				A7DA2080113FECD400BF472F /* ignoregaps.h */,
+				7E962A40121F76B1007464B5 /* invsimpson.h */,
+				7E962A41121F76B1007464B5 /* invsimpson.cpp */,
 				A7DA2083113FECD400BF472F /* jackknife.cpp */,
 				A7DA2084113FECD400BF472F /* jackknife.h */,
 				A7DA2093113FECD400BF472F /* logsd.cpp */,
@@ -574,6 +628,8 @@
 				A7DA20CF113FECD400BF472F /* qstat.h */,
 				A7DA2104113FECD400BF472F /* shannon.cpp */,
 				A7DA2105113FECD400BF472F /* shannon.h */,
+				7E5B28DC121FEFCC0005339C /* shannoneven.h */,
+				7E5B28DD121FEFCC0005339C /* shannoneven.cpp */,
 				A7DA2106113FECD400BF472F /* sharedace.cpp */,
 				A7DA2107113FECD400BF472F /* sharedace.h */,
 				A7DA2108113FECD400BF472F /* sharedanderberg.h */,
@@ -622,6 +678,10 @@
 				A7DA213D113FECD400BF472F /* sharedthetayc.h */,
 				A7DA2140113FECD400BF472F /* shen.cpp */,
 				A7DA2141113FECD400BF472F /* shen.h */,
+				7E4EBD43122018FB00D85E7B /* simpsoneven.h */,
+				7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */,
+				7E5B294A121FFADC0005339C /* smithwilson.h */,
+				7E5B294B121FFADC0005339C /* smithwilson.cpp */,
 				A7DA2142113FECD400BF472F /* simpson.cpp */,
 				A7DA2143113FECD400BF472F /* simpson.h */,
 				A7DA2149113FECD400BF472F /* sobs.h */,
@@ -634,6 +694,7 @@
 				A7DA2170113FECD400BF472F /* uvest.h */,
 				A7DA2179113FECD400BF472F /* weighted.cpp */,
 				A7DA217A113FECD400BF472F /* weighted.h */,
+				7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */,
 				A7DA217B113FECD400BF472F /* whittaker.cpp */,
 				A7DA217C113FECD400BF472F /* whittaker.h */,
 			);
@@ -646,19 +707,19 @@
 				A7DA202B113FECD400BF472F /* command.hpp */,
 				A7DA1FEF113FECD400BF472F /* aligncommand.h */,
 				A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,
-				A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
 				A7DA1FFE113FECD400BF472F /* binsequencecommand.h */,
+				A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
 				A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
 				A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
 				A7D216061199C47F00F13F13 /* catchallcommand.h */,
 				A7D216071199C47F00F13F13 /* catchallcommand.cpp */,
 				A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
-				A78434881162224F00100BE0 /* chimeraccodecommand.h */,
 				A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
 				A7825502116519F70002E2DD /* chimerabellerophoncommand.h */,
 				A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */,
 				A747E79B1163442A00FB9042 /* chimeracheckcommand.h */,
 				A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */,
+				A78434881162224F00100BE0 /* chimeraccodecommand.h */,
 				A78434891162224F00100BE0 /* chimeraccodecommand.cpp */,
 				A78254461164D7790002E2DD /* chimerapintailcommand.h */,
 				A78254471164D7790002E2DD /* chimerapintailcommand.cpp */,
@@ -668,16 +729,22 @@
 				A73953DB11987ED100B0B160 /* chopseqscommand.cpp */,
 				A7DA201E113FECD400BF472F /* classifyseqscommand.h */,
 				A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
+				A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */,
+				A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */,
 				A7D215C811996C6E00F13F13 /* clearcutcommand.h */,
 				A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
 				A7DA2021113FECD400BF472F /* clustercommand.cpp */,
 				A7DA2022113FECD400BF472F /* clustercommand.h */,
-				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
+				A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
+				A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
 				A7DA2026113FECD400BF472F /* collectcommand.h */,
+				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
 				A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
 				A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
 				A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
 				A7DA2032113FECD400BF472F /* consensuscommand.h */,
+				A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
+				A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
 				A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
 				A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
 				A7DA203E113FECD400BF472F /* distancecommand.cpp */,
@@ -688,12 +755,14 @@
 				A7DA205B113FECD400BF472F /* getgroupcommand.h */,
 				A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
 				A7DA205D113FECD400BF472F /* getlabelcommand.h */,
-				A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
 				A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
-				A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
+				A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
 				A7DA2061113FECD400BF472F /* getoturepcommand.h */,
+				A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
 				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
 				A7DA2063113FECD400BF472F /* getrabundcommand.h */,
+				A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */,
+				A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */,
 				A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
 				A7DA2065113FECD400BF472F /* getsabundcommand.h */,
 				A7DA2067113FECD400BF472F /* getseqscommand.h */,
@@ -758,16 +827,22 @@
 				A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
 				A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */,
 				A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
+				7EA299BA11E384940022D8D3 /* sensspeccommand.h */,
+				7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */,
+				7E84528511EF4BEB00564975 /* seqerrorcommand.h */,
+				7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */,
 				A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
 				A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
 				A7DA2103113FECD400BF472F /* setdircommand.h */,
 				A7DA2102113FECD400BF472F /* setdircommand.cpp */,
 				A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
 				A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
+				A732505E11E49EF100484B90 /* sffinfocommand.h */,
+				A732505F11E49EF100484B90 /* sffinfocommand.cpp */,
 				A7DA2110113FECD400BF472F /* sharedcommand.h */,
 				A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
-				A73F163411A1951D0087CA57 /* splitabundcommand.h */,
-				A73F163511A1951D0087CA57 /* splitabundcommand.cpp */,
+				A71D924511AEB42400D00CBC /* splitabundcommand.h */,
+				A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
 				A7DA2155113FECD400BF472F /* summarycommand.h */,
 				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
 				A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
@@ -818,8 +893,10 @@
 				A7DA20A3113FECD400BF472F /* nameassignment.hpp */,
 				A7DA20B6113FECD400BF472F /* ordervector.cpp */,
 				A7DA20B7113FECD400BF472F /* ordervector.hpp */,
-				A7DA20D2113FECD400BF472F /* rabundvector.cpp */,
+				7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */,
+				7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */,
 				A7DA20D3113FECD400BF472F /* rabundvector.hpp */,
+				A7DA20D2113FECD400BF472F /* rabundvector.cpp */,
 				A7DA20F6113FECD400BF472F /* sabundvector.cpp */,
 				A7DA20F7113FECD400BF472F /* sabundvector.hpp */,
 				A7DA20FE113FECD400BF472F /* sequence.cpp */,
@@ -832,8 +909,10 @@
 				A7DA212B113FECD400BF472F /* sharedordervector.h */,
 				A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */,
 				A7DA212D113FECD400BF472F /* sharedrabundvector.h */,
-				A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
+				A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */,
+				A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */,
 				A7DA212F113FECD400BF472F /* sharedsabundvector.h */,
+				A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
 				A7DA214C113FECD400BF472F /* sparsematrix.cpp */,
 				A7DA214D113FECD400BF472F /* sparsematrix.hpp */,
 				A7DA214E113FECD400BF472F /* suffixdb.cpp */,
@@ -919,10 +998,35 @@
 				A7DA20ED113FECD400BF472F /* readphylip.h */,
 				A7DA20EE113FECD400BF472F /* readtree.cpp */,
 				A7DA20EF113FECD400BF472F /* readtree.h */,
+				A71D924711AEB42400D00CBC /* splitmatrix.h */,
+				A71D924611AEB42400D00CBC /* splitmatrix.cpp */,
 			);
 			name = read;
 			sourceTree = "<group>";
 		};
+		A7DF0AE5121EBC26004A03EA /* clearcutsource */ = {
+			isa = PBXGroup;
+			children = (
+				A7DF0AD4121EBB14004A03EA /* clearcut.h */,
+				A71BA75F1225694E00C57506 /* clearcut.cpp */,
+				A7DF0AD7121EBB14004A03EA /* common.h */,
+				A7DF0AD8121EBB14004A03EA /* dayhoff.h */,
+				A7DF0AD6121EBB14004A03EA /* cmdargs.h */,
+				A7DF0AD5121EBB14004A03EA /* cmdargs.cpp */,
+				A7DF0AD9121EBB14004A03EA /* distclearcut.cpp */,
+				A7DF0ADA121EBB14004A03EA /* distclearcut.h */,
+				A7DF0ADB121EBB14004A03EA /* dmat.cpp */,
+				A7DF0ADC121EBB14004A03EA /* dmat.h */,
+				A7DF0ADD121EBB14004A03EA /* fasta.cpp */,
+				A7DF0ADE121EBB14004A03EA /* fasta.h */,
+				A7DF0ADF121EBB14004A03EA /* getopt_long.cpp */,
+				A7DF0AE0121EBB14004A03EA /* getopt_long.h */,
+				A7DF0AE2121EBB14004A03EA /* prng.h */,
+				A7DF0AE1121EBB14004A03EA /* prng.cpp */,
+			);
+			name = clearcutsource;
+			sourceTree = "<group>";
+		};
 /* End PBXGroup section */
 
 /* Begin PBXLegacyTarget section */
@@ -946,6 +1050,7 @@
 			isa = PBXProject;
 			attributes = {
 				BuildIndependentTargetsInParallel = YES;
+				ORGANIZATIONNAME = "Schloss Lab";
 			};
 			buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
 			compatibilityVersion = "Xcode 3.0";
@@ -983,7 +1088,7 @@
 				GCC_WARN_UNUSED_VARIABLE = YES;
 				LINK_WITH_STANDARD_LIBRARIES = YES;
 				PREBINDING = NO;
-				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.6.sdk";
 			};
 			name = Release;
 		};