X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=1c282d96b81dd6ee49eb177225076ffa91ef8894;hb=cbb336d5650cfe1f83a398a837794dcfbbbd3756;hp=ab546df5272e5ed9044d1fb1d8bc053748579e9a;hpb=0d714b1c40488d4c2f3a61a5ef861f21522d48b4;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index ab546df..1c282d9 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,35 +7,85 @@
 	objects = {
 
 /* Begin PBXFileReference section */
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@@ -440,14 +490,38 @@
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 		A7DA217C113FECD400BF472F /* whittaker.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = whittaker.h; sourceTree = "<group>"; };
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+		A7F6C8EB12423C0300299875 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = "<group>"; };
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 /* End PBXFileReference section */
 
 /* Begin PBXGroup section */
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 			isa = PBXGroup;
 			children = (
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 				A7639F8D1175DF35008F5578 /* makefile */,
 				A7DA1FF0113FECD400BF472F /* alignment.cpp */,
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@@ -456,9 +530,12 @@
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 				A7DA201F113FECD400BF472F /* cluster.cpp */,
 				A7DA2020113FECD400BF472F /* cluster.hpp */,
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+				A72E295E127ADCE300905B79 /* clusterclassic.cpp */,
 				A7CB593B11402EF90010EB83 /* calculators */,
 				A7CB594A11402FB40010EB83 /* chimeras */,
 				A7CB594511402F6E0010EB83 /* classifers */,
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 				A7CB593E11402F110010EB83 /* commands */,
 				A7CB594211402F430010EB83 /* containers */,
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@@ -473,6 +550,7 @@
 				A7DA203C113FECD400BF472F /* display.h */,
 				A7DA2042113FECD400BF472F /* dlibshuff.cpp */,
 				A7DA2043113FECD400BF472F /* dlibshuff.h */,
+				A780E6CB11E7745D00BB5718 /* endiannessmacros.h */,
 				A7DA2048113FECD400BF472F /* engine.cpp */,
 				A7DA2049113FECD400BF472F /* engine.hpp */,
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@@ -491,6 +569,7 @@
 				A7DA2082113FECD400BF472F /* inputdata.h */,
 				A7DA208B113FECD400BF472F /* libshuff.cpp */,
 				A7DA208C113FECD400BF472F /* libshuff.h */,
+				A7F6C8DC1242299300299875 /* metastatsource */,
 				A7DA209E113FECD400BF472F /* mothur.cpp */,
 				A7DA209F113FECD400BF472F /* mothur.h */,
 				A7DA20A0113FECD400BF472F /* mothurout.cpp */,
@@ -562,7 +641,11 @@
 				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 */,
@@ -580,6 +663,8 @@
 				A7DA20CF113FECD400BF472F /* qstat.h */,
 				A7DA2104113FECD400BF472F /* shannon.cpp */,
 				A7DA2105113FECD400BF472F /* shannon.h */,
+				7E5B28DC121FEFCC0005339C /* shannoneven.h */,
+				7E5B28DD121FEFCC0005339C /* shannoneven.cpp */,
 				A7DA2106113FECD400BF472F /* sharedace.cpp */,
 				A7DA2107113FECD400BF472F /* sharedace.h */,
 				A7DA2108113FECD400BF472F /* sharedanderberg.h */,
@@ -628,6 +713,10 @@
 				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 */,
@@ -640,6 +729,7 @@
 				A7DA2170113FECD400BF472F /* uvest.h */,
 				A7DA2179113FECD400BF472F /* weighted.cpp */,
 				A7DA217A113FECD400BF472F /* weighted.h */,
+				7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */,
 				A7DA217B113FECD400BF472F /* whittaker.cpp */,
 				A7DA217C113FECD400BF472F /* whittaker.h */,
 			);
@@ -654,17 +744,17 @@
 				A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,
 				A7DA1FFE113FECD400BF472F /* binsequencecommand.h */,
 				A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
-				A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
 				A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
+				A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
 				A7D216061199C47F00F13F13 /* catchallcommand.h */,
 				A7D216071199C47F00F13F13 /* catchallcommand.cpp */,
-				A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
-				A78434881162224F00100BE0 /* chimeraccodecommand.h */,
 				A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
+				A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
 				A7825502116519F70002E2DD /* chimerabellerophoncommand.h */,
 				A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */,
 				A747E79B1163442A00FB9042 /* chimeracheckcommand.h */,
 				A747E79C1163442A00FB9042 /* chimeracheckcommand.cpp */,
+				A78434881162224F00100BE0 /* chimeraccodecommand.h */,
 				A78434891162224F00100BE0 /* chimeraccodecommand.cpp */,
 				A78254461164D7790002E2DD /* chimerapintailcommand.h */,
 				A78254471164D7790002E2DD /* chimerapintailcommand.cpp */,
@@ -678,74 +768,96 @@
 				A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */,
 				A7D215C811996C6E00F13F13 /* clearcutcommand.h */,
 				A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
-				A7DA2021113FECD400BF472F /* clustercommand.cpp */,
 				A7DA2022113FECD400BF472F /* clustercommand.h */,
+				A7DA2021113FECD400BF472F /* clustercommand.cpp */,
+				A7653D111278B09C009D6C09 /* clusterdoturcommand.h */,
+				A7653D121278B09C009D6C09 /* clusterdoturcommand.cpp */,
+				A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */,
+				A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */,
 				A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
 				A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
-				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
 				A7DA2026113FECD400BF472F /* collectcommand.h */,
-				A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
+				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
 				A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
-				A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
+				A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
 				A7DA2032113FECD400BF472F /* consensuscommand.h */,
-				A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
+				A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
+				A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
+				A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
 				A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
-				A7DA203E113FECD400BF472F /* distancecommand.cpp */,
+				A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
 				A7DA203F113FECD400BF472F /* distancecommand.h */,
-				A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
+				A7DA203E113FECD400BF472F /* distancecommand.cpp */,
+				A76714DD126DE45A003F359A /* deuniqueseqscommand.h */,
+				A76714DE126DE45A003F359A /* deuniqueseqscommand.cpp */,
 				A7DA2050113FECD400BF472F /* filterseqscommand.h */,
-				A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
+				A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
 				A7DA205B113FECD400BF472F /* getgroupcommand.h */,
-				A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
+				A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
 				A7DA205D113FECD400BF472F /* getlabelcommand.h */,
+				A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
+				A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
+				A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
 				A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
 				A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
 				A7DA2061113FECD400BF472F /* getoturepcommand.h */,
 				A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
-				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
 				A7DA2063113FECD400BF472F /* getrabundcommand.h */,
-				A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
+				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
+				A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */,
+				A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */,
 				A7DA2065113FECD400BF472F /* getsabundcommand.h */,
+				A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
 				A7DA2067113FECD400BF472F /* getseqscommand.h */,
 				A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
-				A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
 				A7DA2069113FECD400BF472F /* getsharedotucommand.h */,
-				A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
+				A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
 				A7DA2075113FECD400BF472F /* hclustercommand.h */,
-				A7DA2078113FECD400BF472F /* heatmapcommand.cpp */,
+				A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
 				A7DA2079113FECD400BF472F /* heatmapcommand.h */,
-				A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */,
+				A7DA2078113FECD400BF472F /* heatmapcommand.cpp */,
 				A7DA207D113FECD400BF472F /* heatmapsimcommand.h */,
-				A7DA207E113FECD400BF472F /* helpcommand.cpp */,
+				A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */,
 				A7DA207F113FECD400BF472F /* helpcommand.h */,
-				A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
+				A7DA207E113FECD400BF472F /* helpcommand.cpp */,
 				A7DA208E113FECD400BF472F /* libshuffcommand.h */,
+				A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
 				A7DA2090113FECD400BF472F /* listseqscommand.h */,
 				A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
 				A703FE931194645F002C397E /* makegroupcommand.h */,
 				A703FE941194645F002C397E /* makegroupcommand.cpp */,
-				A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
 				A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
-				A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
+				A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
 				A7DA209B113FECD400BF472F /* mergefilecommand.h */,
-				A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
+				A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
+				A7F6C8EA12423C0300299875 /* metastatscommand.h */,
+				A7F6C8EB12423C0300299875 /* metastatscommand.cpp */,
 				A7DA209D113FECD400BF472F /* mgclustercommand.h */,
-				A7DA20AC113FECD400BF472F /* nocommands.cpp */,
+				A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
 				A7DA20AD113FECD400BF472F /* nocommands.h */,
-				A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
+				A7DA20AC113FECD400BF472F /* nocommands.cpp */,
+				A798626D1240D91B005FC847 /* normalizesharedcommand.h */,
+				A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
 				A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
-				A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
+				A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
+				A77D787B126F387700F351BD /* pairwiseseqscommand.h */,
+				A77D787C126F387700F351BD /* pairwiseseqscommand.cpp */,
+				A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */,
+				A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */,
 				A7DA20BD113FECD400BF472F /* parselistscommand.h */,
-				A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
+				A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
 				A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
-				A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
+				A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
 				A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
+				A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
 				A7DA20C3113FECD400BF472F /* pcacommand.h */,
 				A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
 				A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */,
 				A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */,
 				A7DA20C7113FECD400BF472F /* phylotypecommand.h */,
 				A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
+				A72C66A1125B356F0058C2F9 /* pipelinepdscommand.h */,
+				A72C66A2125B356F0058C2F9 /* pipelinepdscommand.cpp */,
 				A7DA20CB113FECD400BF472F /* preclustercommand.h */,
 				A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
 				A7DA20D1113FECD400BF472F /* quitcommand.h */,
@@ -760,6 +872,8 @@
 				A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
 				A7DA20F1113FECD400BF472F /* readtreecommand.h */,
 				A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+				A787A28E124CE1470076EB84 /* removelineagecommand.h */,
+				A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
 				A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
 				A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
 				A7DA20F5113FECD400BF472F /* reversecommand.h */,
@@ -768,16 +882,26 @@
 				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 */,
 				A71D924511AEB42400D00CBC /* splitabundcommand.h */,
 				A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
+				A7F139481247C3CB0033324C /* splitgroupscommand.h */,
+				A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
+				A7653CB112789EFD009D6C09 /* subsamplecommand.h */,
+				A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */,
 				A7DA2155113FECD400BF472F /* summarycommand.h */,
 				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
 				A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
@@ -828,8 +952,10 @@
 				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 */,
@@ -842,8 +968,10 @@
 				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 */,
@@ -935,6 +1063,40 @@
 			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>";
+		};
+		A7F6C8DC1242299300299875 /* metastatsource */ = {
+			isa = PBXGroup;
+			children = (
+				A7F6C8E2124229F900299875 /* fisher2.h */,
+				A7F6C8E1124229F900299875 /* fisher2.c */,
+				A7F6C9D512425D4600299875 /* metastats.h */,
+				A7F6C8E3124229F900299875 /* metastats2.c */,
+			);
+			name = metastatsource;
+			sourceTree = "<group>";
+		};
 /* End PBXGroup section */
 
 /* Begin PBXLegacyTarget section */
@@ -958,10 +1120,18 @@
 			isa = PBXProject;
 			attributes = {
 				BuildIndependentTargetsInParallel = YES;
+				ORGANIZATIONNAME = "Schloss Lab";
 			};
 			buildConfigurationList = 1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */;
 			compatibilityVersion = "Xcode 3.0";
+			developmentRegion = English;
 			hasScannedForEncodings = 1;
+			knownRegions = (
+				English,
+				Japanese,
+				French,
+				German,
+			);
 			mainGroup = 08FB7794FE84155DC02AAC07 /* mothur */;
 			projectDirPath = "";
 			projectRoot = "";