X-Git-Url: https://git.donarmstrong.com/?a=blobdiff_plain;f=Mothur.xcodeproj%2Fproject.pbxproj;h=72be7732a88856925aa54c085ed92389c1272d0a;hb=bf83aa09a52403a2faf1a1f82489d1e0c8c32283;hp=e30c0d4acd457fb66f0a21b289853eb7578b310a;hpb=99c986582ae659c205411639a8e9fa88fb680cd0;p=mothur.git

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index e30c0d4..72be773 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -7,6 +7,145 @@
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+		A7D216061199C47F00F13F13 /* catchallcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = catchallcommand.h; sourceTree = "<group>"; };
+		A7D216071199C47F00F13F13 /* catchallcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = catchallcommand.cpp; sourceTree = "<group>"; };
+		A7D9006D12C2544A00D8F543 /* corraxescommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = corraxescommand.h; sourceTree = "<group>"; };
+		A7D9006E12C2544A00D8F543 /* corraxescommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = corraxescommand.cpp; sourceTree = "<group>"; };
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@@ -405,12 +544,47 @@
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 		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>"; };
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+		A7DF0AE2121EBB14004A03EA /* prng.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = prng.h; sourceTree = "<group>"; };
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+		A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsesffcommand.h; sourceTree = "<group>"; };
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+		A7F0C06512B7D64F0048BC64 /* odum.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = odum.cpp; sourceTree = "<group>"; };
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+		A7F0C10212B80EEC0048BC64 /* structeuclidean.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = structeuclidean.cpp; sourceTree = "<group>"; };
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+		A7F139491247C3CB0033324C /* splitgroupscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = splitgroupscommand.cpp; sourceTree = "<group>"; };
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+		A7F6C8EA12423C0300299875 /* metastatscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastatscommand.h; sourceTree = "<group>"; };
+		A7F6C8EB12423C0300299875 /* metastatscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = metastatscommand.cpp; sourceTree = "<group>"; };
+		A7F6C9D512425D4600299875 /* metastats.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = metastats.h; sourceTree = "<group>"; };
 /* End PBXFileReference section */
 
 /* Begin PBXGroup section */
 		08FB7794FE84155DC02AAC07 /* mothur */ = {
 			isa = PBXGroup;
 			children = (
+				7E99D77C12CBAD780041246B /* untitled.h */,
+				7E99D77D12CBAD780041246B /* untitled.cpp */,
+				A768D95D1248FEAA008AB1D0 /* mothur */,
+				A7639F8D1175DF35008F5578 /* makefile */,
 				A7DA1FF0113FECD400BF472F /* alignment.cpp */,
 				A7DA1FF1113FECD400BF472F /* alignment.hpp */,
 				A7DA1FF6113FECD400BF472F /* averagelinkage.cpp */,
@@ -418,9 +592,12 @@
 				A7DA1FFF113FECD400BF472F /* blastalign.cpp */,
 				A7DA201F113FECD400BF472F /* cluster.cpp */,
 				A7DA2020113FECD400BF472F /* cluster.hpp */,
+				A72E295D127ADCE300905B79 /* clusterclassic.h */,
+				A72E295E127ADCE300905B79 /* clusterclassic.cpp */,
 				A7CB593B11402EF90010EB83 /* calculators */,
 				A7CB594A11402FB40010EB83 /* chimeras */,
 				A7CB594511402F6E0010EB83 /* classifers */,
+				A7DF0AE5121EBC26004A03EA /* clearcutsource */,
 				A7CB593E11402F110010EB83 /* commands */,
 				A7CB594211402F430010EB83 /* containers */,
 				A7DA2023113FECD400BF472F /* collect.cpp */,
@@ -435,6 +612,7 @@
 				A7DA203C113FECD400BF472F /* display.h */,
 				A7DA2042113FECD400BF472F /* dlibshuff.cpp */,
 				A7DA2043113FECD400BF472F /* dlibshuff.h */,
+				A780E6CB11E7745D00BB5718 /* endiannessmacros.h */,
 				A7DA2048113FECD400BF472F /* engine.cpp */,
 				A7DA2049113FECD400BF472F /* engine.hpp */,
 				A7DA204C113FECD400BF472F /* fileoutput.cpp */,
@@ -453,6 +631,7 @@
 				A7DA2082113FECD400BF472F /* inputdata.h */,
 				A7DA208B113FECD400BF472F /* libshuff.cpp */,
 				A7DA208C113FECD400BF472F /* libshuff.h */,
+				A7F6C8DC1242299300299875 /* metastatsource */,
 				A7DA209E113FECD400BF472F /* mothur.cpp */,
 				A7DA209F113FECD400BF472F /* mothur.h */,
 				A7DA20A0113FECD400BF472F /* mothurout.cpp */,
@@ -491,6 +670,10 @@
 				A7DA2174113FECD400BF472F /* validparameter.h */,
 				A7DA2175113FECD400BF472F /* venn.cpp */,
 				A7DA2176113FECD400BF472F /* venn.h */,
+				7E13BDD112BE3FEE004B8A53 /* reportfile.h */,
+				7E13BDD212BE3FEF004B8A53 /* reportfile.cpp */,
+				7E1CA7D712C2A384003F10B2 /* flowdata.h */,
+				7E1CA7D812C2A384003F10B2 /* flowdata.cpp */,
 			);
 			name = mothur;
 			sourceTree = "<group>";
@@ -498,6 +681,8 @@
 		A7CB593B11402EF90010EB83 /* calculators */ = {
 			isa = PBXGroup;
 			children = (
+				7E99CA1312C8B0970041246B /* shhhercommand.h */,
+				7E99CA1412C8B0970041246B /* shhhercommand.cpp */,
 				A7DA200B113FECD400BF472F /* calculator.cpp */,
 				A7DA200C113FECD400BF472F /* calculator.h */,
 				A7DA1FED113FECD400BF472F /* ace.h */,
@@ -510,6 +695,8 @@
 				A7DA2006113FECD400BF472F /* bootstrap.h */,
 				A7DA2009113FECD400BF472F /* bstick.cpp */,
 				A7DA200A113FECD400BF472F /* bstick.h */,
+				A7F0C08A12B7EAE80048BC64 /* canberra.h */,
+				A7F0C08B12B7EAE80048BC64 /* canberra.cpp */,
 				A7DA200F113FECD400BF472F /* chao1.cpp */,
 				A7DA2010113FECD400BF472F /* chao1.h */,
 				A7DA2033113FECD400BF472F /* coverage.cpp */,
@@ -524,22 +711,48 @@
 				A7DA2059113FECD400BF472F /* geom.h */,
 				A7DA206C113FECD400BF472F /* goodscoverage.cpp */,
 				A7DA206D113FECD400BF472F /* goodscoverage.h */,
+				A7BB565F12BBB0480041F26F /* gower.h */,
+				A7BB566012BBB0480041F26F /* gower.cpp */,
+				A7460B7812B9444800866BB6 /* hamming.h */,
+				A7460B7912B9444800866BB6 /* hamming.cpp */,
+				7E5B2917121FF53C0005339C /* heip.h */,
+				7E5B2918121FF53C0005339C /* heip.cpp */,
+				A7460A7312B8FCDC00866BB6 /* hellinger.h */,
+				A7460A7412B8FCDC00866BB6 /* hellinger.cpp */,
 				A7DA2080113FECD400BF472F /* ignoregaps.h */,
+				7E962A40121F76B1007464B5 /* invsimpson.h */,
+				7E962A41121F76B1007464B5 /* invsimpson.cpp */,
 				A7DA2083113FECD400BF472F /* jackknife.cpp */,
 				A7DA2084113FECD400BF472F /* jackknife.h */,
 				A7DA2093113FECD400BF472F /* logsd.cpp */,
 				A7DA2094113FECD400BF472F /* logsd.h */,
+				A7460A9812B9061B00866BB6 /* manhattan.h */,
+				A7460A9912B9061B00866BB6 /* manhattan.cpp */,
+				A7BB56B812BBB5690041F26F /* memchi2.h */,
+				A7BB56B912BBB5690041F26F /* memchi2.cpp */,
+				A7BB56EB12BBBFDF0041F26F /* memchord.h */,
+				A7BB56EC12BBBFDF0041F26F /* memchord.cpp */,
+				A7BB570B12BBC2880041F26F /* memeuclidean.h */,
+				A7BB570C12BBC2880041F26F /* memeuclidean.cpp */,
+				A7BB573712BBC43B0041F26F /* mempearson.h */,
+				A7BB573812BBC43B0041F26F /* mempearson.cpp */,
 				A7DA20AE113FECD400BF472F /* npshannon.cpp */,
 				A7DA20AF113FECD400BF472F /* npshannon.h */,
 				A7DA20B0113FECD400BF472F /* nseqs.h */,
+				A7F0C06412B7D64F0048BC64 /* odum.h */,
+				A7F0C06512B7D64F0048BC64 /* odum.cpp */,
 				A7DA20B2113FECD400BF472F /* onegapdist.h */,
 				A7DA20B3113FECD400BF472F /* onegapignore.h */,
+				A72B3A7B118B4D1B004B9F8D /* phylodiversity.h */,
+				A72B3A7C118B4D1B004B9F8D /* phylodiversity.cpp */,
 				A7DA20BE113FECD400BF472F /* parsimony.cpp */,
 				A7DA20BF113FECD400BF472F /* parsimony.h */,
 				A7DA20CE113FECD400BF472F /* qstat.cpp */,
 				A7DA20CF113FECD400BF472F /* qstat.h */,
 				A7DA2104113FECD400BF472F /* shannon.cpp */,
 				A7DA2105113FECD400BF472F /* shannon.h */,
+				7E5B28DC121FEFCC0005339C /* shannoneven.h */,
+				7E5B28DD121FEFCC0005339C /* shannoneven.cpp */,
 				A7DA2106113FECD400BF472F /* sharedace.cpp */,
 				A7DA2107113FECD400BF472F /* sharedace.h */,
 				A7DA2108113FECD400BF472F /* sharedanderberg.h */,
@@ -588,11 +801,31 @@
 				A7DA213D113FECD400BF472F /* sharedthetayc.h */,
 				A7DA2140113FECD400BF472F /* shen.cpp */,
 				A7DA2141113FECD400BF472F /* shen.h */,
-				A7DA2142113FECD400BF472F /* simpson.cpp */,
+				7E4EBD43122018FB00D85E7B /* simpsoneven.h */,
+				7E4EBD44122018FB00D85E7B /* simpsoneven.cpp */,
+				7E5B294A121FFADC0005339C /* smithwilson.h */,
+				7E5B294B121FFADC0005339C /* smithwilson.cpp */,
 				A7DA2143113FECD400BF472F /* simpson.h */,
+				A7DA2142113FECD400BF472F /* simpson.cpp */,
 				A7DA2149113FECD400BF472F /* sobs.h */,
+				A7460ADB12B914B700866BB6 /* soergel.h */,
+				A7460ADC12B914B700866BB6 /* soergel.cpp */,
 				A7DA214A113FECD400BF472F /* solow.cpp */,
 				A7DA214B113FECD400BF472F /* solow.h */,
+				A7460B5912B93F1F00866BB6 /* speciesprofile.h */,
+				A7460B5A12B93F1F00866BB6 /* speciesprofile.cpp */,
+				A7460AF712B9218400866BB6 /* spearman.h */,
+				A7460AF812B9218400866BB6 /* spearman.cpp */,
+				A7BB555212BB87F30041F26F /* structchi2.h */,
+				A7BB555312BB87F30041F26F /* structchi2.cpp */,
+				A7460A3F12B8EF1C00866BB6 /* structchord.h */,
+				A7460A4012B8EF1C00866BB6 /* structchord.cpp */,
+				A7F0C10112B80EEC0048BC64 /* structeuclidean.h */,
+				A7F0C10212B80EEC0048BC64 /* structeuclidean.cpp */,
+				A7460B3612B9377400866BB6 /* structkulczynski.h */,
+				A7460B3712B9377400866BB6 /* structkulczynski.cpp */,
+				A7460AC912B90C5600866BB6 /* structpearson.h */,
+				A7460ACA12B90C5600866BB6 /* structpearson.cpp */,
 				A7DA2160113FECD400BF472F /* treecalculator.h */,
 				A7DA216D113FECD400BF472F /* unweighted.cpp */,
 				A7DA216E113FECD400BF472F /* unweighted.h */,
@@ -600,6 +833,7 @@
 				A7DA2170113FECD400BF472F /* uvest.h */,
 				A7DA2179113FECD400BF472F /* weighted.cpp */,
 				A7DA217A113FECD400BF472F /* weighted.h */,
+				7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */,
 				A7DA217B113FECD400BF472F /* whittaker.cpp */,
 				A7DA217C113FECD400BF472F /* whittaker.h */,
 			);
@@ -609,121 +843,201 @@
 		A7CB593E11402F110010EB83 /* commands */ = {
 			isa = PBXGroup;
 			children = (
+				7E1CA7D912C2A425003F10B2 /* trimflowscommand.h */,
+				7E1CA7DA12C2A425003F10B2 /* trimflowscommand.cpp */,
 				A7DA202B113FECD400BF472F /* command.hpp */,
 				A7DA1FEF113FECD400BF472F /* aligncommand.h */,
 				A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,
-				A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
 				A7DA1FFE113FECD400BF472F /* binsequencecommand.h */,
-				A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
+				A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
 				A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
-				A7DA2017113FECD400BF472F /* chimeraseqscommand.cpp */,
+				A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
+				A7D216061199C47F00F13F13 /* catchallcommand.h */,
+				A7D216071199C47F00F13F13 /* catchallcommand.cpp */,
 				A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
-				A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
+				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 */,
+				A747E81C116365E000FB9042 /* chimeraslayercommand.h */,
+				A747E81D116365E000FB9042 /* chimeraslayercommand.cpp */,
+				A73953DA11987ED100B0B160 /* chopseqscommand.h */,
+				A73953DB11987ED100B0B160 /* chopseqscommand.cpp */,
 				A7DA201E113FECD400BF472F /* classifyseqscommand.h */,
-				A7DA2021113FECD400BF472F /* clustercommand.cpp */,
+				A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
+				A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */,
+				A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */,
+				A7D215C811996C6E00F13F13 /* clearcutcommand.h */,
+				A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
 				A7DA2022113FECD400BF472F /* clustercommand.h */,
-				A7DA2025113FECD400BF472F /* collectcommand.cpp */,
+				A7DA2021113FECD400BF472F /* clustercommand.cpp */,
+				A7653D111278B09C009D6C09 /* clusterdoturcommand.h */,
+				A7653D121278B09C009D6C09 /* clusterdoturcommand.cpp */,
+				A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */,
+				A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */,
+				A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
+				A71D924211AEB42400D00CBC /* clustersplitcommand.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 */,
+				A71FF438129BDC35004397E6 /* consensusseqscommand.h */,
+				A71FF439129BDC35004397E6 /* consensusseqscommand.cpp */,
+				A7D9006D12C2544A00D8F543 /* corraxescommand.h */,
+				A7D9006E12C2544A00D8F543 /* corraxescommand.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 */,
+				A75103D6128AE34100ABB831 /* getgroupscommand.h */,
+				A75103D7128AE34100ABB831 /* getgroupscommand.cpp */,
 				A7DA205D113FECD400BF472F /* getlabelcommand.h */,
-				A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
+				A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
+				A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
+				A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
 				A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
-				A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
+				A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
+				A7510407128AFCC100ABB831 /* getotuscommand.h */,
+				A7510408128AFCC100ABB831 /* getotuscommand.cpp */,
 				A7DA2061113FECD400BF472F /* getoturepcommand.h */,
-				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
+				A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
 				A7DA2063113FECD400BF472F /* getrabundcommand.h */,
-				A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
+				A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
+				A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */,
+				A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */,
 				A7DA2065113FECD400BF472F /* getsabundcommand.h */,
-				A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
+				A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
 				A7DA2067113FECD400BF472F /* getseqscommand.h */,
-				A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
+				A7DA2066113FECD400BF472F /* getseqscommand.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 */,
+				A76D1473128D9DA2005D4DFE /* indicatorcommand.h */,
+				A76D1474128D9DA2005D4DFE /* indicatorcommand.cpp */,
 				A7DA208E113FECD400BF472F /* libshuffcommand.h */,
-				A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
+				A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
 				A7DA2090113FECD400BF472F /* listseqscommand.h */,
-				A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
+				A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
+				A703FE931194645F002C397E /* makegroupcommand.h */,
+				A703FE941194645F002C397E /* makegroupcommand.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 */,
-				A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
+				A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
+				A7E8338C115BBDAA00739EC4 /* parsesffcommand.h */,
+				A7E8338B115BBDAA00739EC4 /* parsesffcommand.cpp */,
 				A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
-				A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
+				A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
 				A7DA20C3113FECD400BF472F /* pcacommand.h */,
-				A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
+				A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
+				A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */,
+				A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */,
 				A7DA20C7113FECD400BF472F /* phylotypecommand.h */,
-				A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
+				A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
+				A72C66A1125B356F0058C2F9 /* pipelinepdscommand.h */,
+				A72C66A2125B356F0058C2F9 /* pipelinepdscommand.cpp */,
 				A7DA20CB113FECD400BF472F /* preclustercommand.h */,
-				A7DA20D0113FECD400BF472F /* quitcommand.cpp */,
+				A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
 				A7DA20D1113FECD400BF472F /* quitcommand.h */,
-				A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */,
+				A7DA20D0113FECD400BF472F /* quitcommand.cpp */,
 				A7DA20DB113FECD400BF472F /* rarefactcommand.h */,
-				A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */,
+				A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */,
 				A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */,
-				A7DA20E5113FECD400BF472F /* readdistcommand.cpp */,
+				A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */,
 				A7DA20E6113FECD400BF472F /* readdistcommand.h */,
-				A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
+				A7DA20E5113FECD400BF472F /* readdistcommand.cpp */,
 				A7DA20EB113FECD400BF472F /* readotucommand.h */,
-				A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+				A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
 				A7DA20F1113FECD400BF472F /* readtreecommand.h */,
-				A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
+				A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
+				A751032A128AC93F00ABB831 /* removegroupscommand.h */,
+				A751032B128AC93F00ABB831 /* removegroupscommand.cpp */,
+				A787A28E124CE1470076EB84 /* removelineagecommand.h */,
+				A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
+				A76D1451128D6A03005D4DFE /* removeotuscommand.h */,
+				A76D1452128D6A03005D4DFE /* removeotuscommand.cpp */,
 				A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
-				A7DA20F4113FECD400BF472F /* reversecommand.cpp */,
+				A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
 				A7DA20F5113FECD400BF472F /* reversecommand.h */,
-				A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
+				A7DA20F4113FECD400BF472F /* reversecommand.cpp */,
 				A7DA20F9113FECD400BF472F /* screenseqscommand.h */,
-				A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
+				A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
 				A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */,
-				A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
+				A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
+				7EA299BA11E384940022D8D3 /* sensspeccommand.h */,
+				7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */,
+				7E84528511EF4BEB00564975 /* seqerrorcommand.h */,
+				7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */,
 				A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
-				A7DA2102113FECD400BF472F /* setdircommand.cpp */,
+				A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
 				A7DA2103113FECD400BF472F /* setdircommand.h */,
-				A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
+				A7DA2102113FECD400BF472F /* setdircommand.cpp */,
+				A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
+				A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
+				A732505E11E49EF100484B90 /* sffinfocommand.h */,
+				A732505F11E49EF100484B90 /* sffinfocommand.cpp */,
 				A7DA2110113FECD400BF472F /* sharedcommand.h */,
-				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
+				A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
+				A71D924511AEB42400D00CBC /* splitabundcommand.h */,
+				A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
+				A7F139481247C3CB0033324C /* splitgroupscommand.h */,
+				A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
+				A7653CB112789EFD009D6C09 /* subsamplecommand.h */,
+				A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */,
 				A7DA2155113FECD400BF472F /* summarycommand.h */,
-				A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */,
+				A7DA2154113FECD400BF472F /* summarycommand.cpp */,
 				A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
-				A7DA215A113FECD400BF472F /* systemcommand.cpp */,
+				A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */,
 				A7DA215B113FECD400BF472F /* systemcommand.h */,
-				A7DA2161113FECD400BF472F /* treegroupscommand.cpp */,
+				A7DA215A113FECD400BF472F /* systemcommand.cpp */,
 				A7DA2162113FECD400BF472F /* treegroupscommand.h */,
-				A7DA2167113FECD400BF472F /* trimseqscommand.cpp */,
+				A7DA2161113FECD400BF472F /* treegroupscommand.cpp */,
 				A7DA2168113FECD400BF472F /* trimseqscommand.h */,
-				A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */,
+				A7DA2167113FECD400BF472F /* trimseqscommand.cpp */,
 				A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */,
-				A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */,
+				A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */,
 				A7DA216C113FECD400BF472F /* unifracweightedcommand.h */,
-				A7DA2177113FECD400BF472F /* venncommand.cpp */,
+				A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */,
 				A7DA2178113FECD400BF472F /* venncommand.h */,
+				A7DA2177113FECD400BF472F /* venncommand.cpp */,
 			);
 			name = commands;
 			sourceTree = "<group>";
@@ -758,8 +1072,10 @@
 				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 */,
@@ -772,8 +1088,10 @@
 				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 */,
@@ -803,6 +1121,8 @@
 				A7DA208A113FECD400BF472F /* knn.h */,
 				A7DA20C4113FECD400BF472F /* phylotree.cpp */,
 				A7DA20C5113FECD400BF472F /* phylotree.h */,
+				A76AAD02117F322B003D8DA1 /* phylosummary.h */,
+				A76AAD03117F322B003D8DA1 /* phylosummary.cpp */,
 				A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */,
 				A7DA215D113FECD400BF472F /* taxonomyequalizer.h */,
 			);
@@ -857,10 +1177,46 @@
 				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>";
+		};
+		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 */
@@ -882,9 +1238,20 @@
 /* Begin PBXProject section */
 		08FB7793FE84155DC02AAC07 /* Project object */ = {
 			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 = "";
@@ -895,23 +1262,6 @@
 /* End PBXProject section */
 
 /* Begin XCBuildConfiguration section */
-		1DEB919008733D9F0010E9CD /* Debug */ = {
-			isa = XCBuildConfiguration;
-			buildSettings = {
-				COPY_PHASE_STRIP = NO;
-				DEBUGGING_SYMBOLS = YES;
-				GCC_DYNAMIC_NO_PIC = NO;
-				GCC_ENABLE_FIX_AND_CONTINUE = YES;
-				GCC_GENERATE_DEBUGGING_SYMBOLS = YES;
-				GCC_OPTIMIZATION_LEVEL = 0;
-				OPTIMIZATION_CFLAGS = "-O0";
-				OTHER_CFLAGS = "";
-				OTHER_LDFLAGS = "";
-				PRODUCT_NAME = mothur;
-				ZERO_LINK = YES;
-			};
-			name = Debug;
-		};
 		1DEB919108733D9F0010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
@@ -924,16 +1274,6 @@
 			};
 			name = Release;
 		};
-		1DEB919408733D9F0010E9CD /* Debug */ = {
-			isa = XCBuildConfiguration;
-			buildSettings = {
-				GCC_WARN_ABOUT_RETURN_TYPE = YES;
-				GCC_WARN_UNUSED_VARIABLE = YES;
-				PREBINDING = NO;
-				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
-			};
-			name = Debug;
-		};
 		1DEB919508733D9F0010E9CD /* Release */ = {
 			isa = XCBuildConfiguration;
 			buildSettings = {
@@ -943,8 +1283,9 @@
 				);
 				GCC_WARN_ABOUT_RETURN_TYPE = YES;
 				GCC_WARN_UNUSED_VARIABLE = YES;
+				LINK_WITH_STANDARD_LIBRARIES = YES;
 				PREBINDING = NO;
-				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
+				SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.6.sdk";
 			};
 			name = Release;
 		};
@@ -954,7 +1295,6 @@
 		1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
-				1DEB919008733D9F0010E9CD /* Debug */,
 				1DEB919108733D9F0010E9CD /* Release */,
 			);
 			defaultConfigurationIsVisible = 0;
@@ -963,7 +1303,6 @@
 		1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
 			isa = XCConfigurationList;
 			buildConfigurations = (
-				1DEB919408733D9F0010E9CD /* Debug */,
 				1DEB919508733D9F0010E9CD /* Release */,
 			);
 			defaultConfigurationIsVisible = 0;