]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added get.otus and remove.otus commands
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 1ac6e0b5a1c87cfdc844e7137da940de80bca6bb..369bae98e626911a3afac441c728b2c469992e85 100644 (file)
                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>"; };
                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>"; };
                A76AAD02117F322B003D8DA1 /* phylosummary.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = phylosummary.h; sourceTree = "<group>"; };
                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; };
+               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>"; };
                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>"; };
                08FB7794FE84155DC02AAC07 /* mothur */ = {
                        isa = PBXGroup;
                        children = (
+                               A768D95D1248FEAA008AB1D0 /* mothur */,
                                A7639F8D1175DF35008F5578 /* makefile */,
                                A7DA1FF0113FECD400BF472F /* alignment.cpp */,
                                A7DA1FF1113FECD400BF472F /* alignment.hpp */,
                                A7DA1FFF113FECD400BF472F /* blastalign.cpp */,
                                A7DA201F113FECD400BF472F /* cluster.cpp */,
                                A7DA2020113FECD400BF472F /* cluster.hpp */,
+                               A72E295D127ADCE300905B79 /* clusterclassic.h */,
+                               A72E295E127ADCE300905B79 /* clusterclassic.cpp */,
                                A7CB593B11402EF90010EB83 /* calculators */,
                                A7CB594A11402FB40010EB83 /* chimeras */,
                                A7CB594511402F6E0010EB83 /* classifers */,
                                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 */,
                                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 */,
                                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 */,
                                A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
                                A7F139481247C3CB0033324C /* splitgroupscommand.h */,
                                A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
+                               A7653CB112789EFD009D6C09 /* subsamplecommand.h */,
+                               A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */,
                                A7DA2155113FECD400BF472F /* summarycommand.h */,
                                A7DA2154113FECD400BF472F /* summarycommand.cpp */,
                                A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
                        };
                        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 = "";