X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=369bae98e626911a3afac441c728b2c469992e85;hb=794b3f789d6160c99b75edb9cf9af5cf3df4b9da;hp=1ac6e0b5a1c87cfdc844e7137da940de80bca6bb;hpb=cea46f0830d8d1a6dc26e3410fc283d26c355831;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 1ac6e0b..369bae9 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -37,10 +37,16 @@
 		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>"; };
+		A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsefastaqcommand.h; sourceTree = "<group>"; };
+		A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = parsefastaqcommand.cpp; 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>"; };
+		A72C66A1125B356F0058C2F9 /* pipelinepdscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pipelinepdscommand.h; sourceTree = "<group>"; };
+		A72C66A2125B356F0058C2F9 /* pipelinepdscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pipelinepdscommand.cpp; sourceTree = "<group>"; };
+		A72E295D127ADCE300905B79 /* clusterclassic.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterclassic.h; sourceTree = "<group>"; };
+		A72E295E127ADCE300905B79 /* clusterclassic.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterclassic.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>"; };
@@ -49,11 +55,30 @@
 		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>"; };
 		A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraslayercommand.cpp; sourceTree = "<group>"; };
+		A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterfragmentscommand.h; sourceTree = "<group>"; };
+		A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterfragmentscommand.cpp; sourceTree = "<group>"; };
+		A751032A128AC93F00ABB831 /* removegroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removegroupscommand.h; sourceTree = "<group>"; };
+		A751032B128AC93F00ABB831 /* removegroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removegroupscommand.cpp; sourceTree = "<group>"; };
+		A75103D6128AE34100ABB831 /* getgroupscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getgroupscommand.h; sourceTree = "<group>"; };
+		A75103D7128AE34100ABB831 /* getgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getgroupscommand.cpp; sourceTree = "<group>"; };
+		A7510407128AFCC100ABB831 /* getotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getotuscommand.h; sourceTree = "<group>"; };
+		A7510408128AFCC100ABB831 /* getotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getotuscommand.cpp; sourceTree = "<group>"; };
 		A7639F8D1175DF35008F5578 /* makefile */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.make; path = makefile; sourceTree = "<group>"; };
+		A7653CB112789EFD009D6C09 /* subsamplecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = subsamplecommand.h; sourceTree = "<group>"; };
+		A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = subsamplecommand.cpp; sourceTree = "<group>"; };
+		A7653D111278B09C009D6C09 /* clusterdoturcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = clusterdoturcommand.h; sourceTree = "<group>"; };
+		A7653D121278B09C009D6C09 /* clusterdoturcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = clusterdoturcommand.cpp; sourceTree = "<group>"; };
+		A76714DD126DE45A003F359A /* deuniqueseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deuniqueseqscommand.h; sourceTree = "<group>"; };
+		A76714DE126DE45A003F359A /* deuniqueseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deuniqueseqscommand.cpp; sourceTree = "<group>"; };
+		A768D95D1248FEAA008AB1D0 /* mothur */ = {isa = PBXFileReference; lastKnownFileType = "compiled.mach-o.executable"; path = mothur; sourceTree = "<group>"; };
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 		A76C4A1011876BAF0009460B /* setlogfilecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = setlogfilecommand.h; sourceTree = SOURCE_ROOT; };
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+		A76D1451128D6A03005D4DFE /* removeotuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeotuscommand.h; sourceTree = "<group>"; };
+		A76D1452128D6A03005D4DFE /* removeotuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeotuscommand.cpp; sourceTree = "<group>"; };
+		A77D787B126F387700F351BD /* pairwiseseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pairwiseseqscommand.h; sourceTree = "<group>"; };
+		A77D787C126F387700F351BD /* pairwiseseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pairwiseseqscommand.cpp; sourceTree = "<group>"; };
 		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>"; };
@@ -61,6 +86,10 @@
 		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>"; };
+		A787A24F124CB46C0076EB84 /* getlineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getlineagecommand.h; sourceTree = "<group>"; };
+		A787A250124CB46C0076EB84 /* getlineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getlineagecommand.cpp; sourceTree = "<group>"; };
+		A787A28E124CE1470076EB84 /* removelineagecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removelineagecommand.h; sourceTree = "<group>"; };
+		A787A28F124CE1470076EB84 /* removelineagecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removelineagecommand.cpp; sourceTree = "<group>"; };
 		A798626D1240D91B005FC847 /* normalizesharedcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = normalizesharedcommand.h; sourceTree = "<group>"; };
 		A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = normalizesharedcommand.cpp; sourceTree = "<group>"; };
 		A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedrabundfloatvector.h; sourceTree = "<group>"; };
@@ -500,6 +529,7 @@
 		08FB7794FE84155DC02AAC07 /* mothur */ = {
 			isa = PBXGroup;
 			children = (
+				A768D95D1248FEAA008AB1D0 /* mothur */,
 				A7639F8D1175DF35008F5578 /* makefile */,
 				A7DA1FF0113FECD400BF472F /* alignment.cpp */,
 				A7DA1FF1113FECD400BF472F /* alignment.hpp */,
@@ -508,6 +538,8 @@
 				A7DA1FFF113FECD400BF472F /* blastalign.cpp */,
 				A7DA201F113FECD400BF472F /* cluster.cpp */,
 				A7DA2020113FECD400BF472F /* cluster.hpp */,
+				A72E295D127ADCE300905B79 /* clusterclassic.h */,
+				A72E295E127ADCE300905B79 /* clusterclassic.cpp */,
 				A7CB593B11402EF90010EB83 /* calculators */,
 				A7CB594A11402FB40010EB83 /* chimeras */,
 				A7CB594511402F6E0010EB83 /* classifers */,
@@ -720,12 +752,12 @@
 				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 */,
 				A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
+				A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
 				A7825502116519F70002E2DD /* chimerabellerophoncommand.h */,
 				A7825503116519F70002E2DD /* chimerabellerophoncommand.cpp */,
 				A747E79B1163442A00FB9042 /* chimeracheckcommand.h */,
@@ -744,82 +776,100 @@
 				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 */,
 				A7DA2026113FECD400BF472F /* collectcommand.h */,
 				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
-				A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
 				A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
-				A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
+				A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
 				A7DA2032113FECD400BF472F /* consensuscommand.h */,
+				A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
 				A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
 				A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
-				A7DA203A113FECD400BF472F /* deconvolutecommand.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 */,
+				A75103D6128AE34100ABB831 /* getgroupscommand.h */,
+				A75103D7128AE34100ABB831 /* getgroupscommand.cpp */,
 				A7DA205D113FECD400BF472F /* getlabelcommand.h */,
+				A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
+				A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
+				A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
 				A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
 				A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
+				A7510407128AFCC100ABB831 /* getotuscommand.h */,
+				A7510408128AFCC100ABB831 /* getotuscommand.cpp */,
 				A7DA2061113FECD400BF472F /* getoturepcommand.h */,
 				A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
-				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
 				A7DA2063113FECD400BF472F /* getrabundcommand.h */,
+				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
 				A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */,
 				A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */,
-				A7DA2064113FECD400BF472F /* getsabundcommand.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 */,
+				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 */,
+				A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
 				A7F6C8EA12423C0300299875 /* metastatscommand.h */,
 				A7F6C8EB12423C0300299875 /* metastatscommand.cpp */,
-				A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
 				A7DA209D113FECD400BF472F /* mgclustercommand.h */,
-				A7DA20AC113FECD400BF472F /* nocommands.cpp */,
+				A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
 				A7DA20AD113FECD400BF472F /* nocommands.h */,
+				A7DA20AC113FECD400BF472F /* nocommands.cpp */,
 				A798626D1240D91B005FC847 /* normalizesharedcommand.h */,
 				A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
-				A7DA20B8113FECD400BF472F /* otuhierarchycommand.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 */,
@@ -834,6 +884,12 @@
 				A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
 				A7DA20F1113FECD400BF472F /* readtreecommand.h */,
 				A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+				A751032A128AC93F00ABB831 /* removegroupscommand.h */,
+				A751032B128AC93F00ABB831 /* removegroupscommand.cpp */,
+				A787A28E124CE1470076EB84 /* removelineagecommand.h */,
+				A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
+				A76D1451128D6A03005D4DFE /* removeotuscommand.h */,
+				A76D1452128D6A03005D4DFE /* removeotuscommand.cpp */,
 				A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
 				A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
 				A7DA20F5113FECD400BF472F /* reversecommand.h */,
@@ -860,6 +916,8 @@
 				A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
 				A7F139481247C3CB0033324C /* splitgroupscommand.h */,
 				A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
+				A7653CB112789EFD009D6C09 /* subsamplecommand.h */,
+				A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */,
 				A7DA2155113FECD400BF472F /* summarycommand.h */,
 				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
 				A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
@@ -1082,7 +1140,14 @@
 			};
 			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 = "";