]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added sorted option to get.rabund command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 9da05bcabafbada3ea826ebc5b4e29486a42c9a7..9427eec004a889ab0481a0da9e7d47431367e046 100644 (file)
@@ -38,6 +38,8 @@
                3746109D0F40657600460C57 /* unifracunweightedcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */; };
                3749271D0FD58C840031C06B /* getsabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749271C0FD58C840031C06B /* getsabundcommand.cpp */; };
                3749273F0FD5956B0031C06B /* getrabundcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3749273E0FD5956B0031C06B /* getrabundcommand.cpp */; };
+               374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F2FEA100634B600E97C66 /* bellerophon.cpp */; };
+               374F301310063B6F00E97C66 /* pintail.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 374F301210063B6F00E97C66 /* pintail.cpp */; };
                37519A6B0F80E6EB00FED5E8 /* sharedanderbergs.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */; };
                37519AA10F810D0200FED5E8 /* venncommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AA00F810D0200FED5E8 /* venncommand.cpp */; };
                37519AB50F810FAE00FED5E8 /* venn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37519AB40F810FAE00FED5E8 /* venn.cpp */; };
@@ -55,7 +57,7 @@
                375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1330F9E433D008EF9B8 /* readcolumn.cpp */; };
                375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1350F9E433D008EF9B8 /* readotu.cpp */; };
                375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 375AA1370F9E433D008EF9B8 /* readphylip.cpp */; };
-               377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 377326630FAF16E0007ABB8B /* concensuscommand.cpp */; };
+               377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 377326630FAF16E0007ABB8B /* consensuscommand.cpp */; };
                378598660FDD497000EF9D03 /* heatmapsimcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */; };
                378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378598730FDD4C1500EF9D03 /* heatmapsim.cpp */; };
                378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3785990F0FDD7E8E00EF9D03 /* optionparser.cpp */; };
                3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
                3799A9500FD6A58C00E33EDE /* distancedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3799A94C0FD6A58C00E33EDE /* distancedb.cpp */; };
                3799A9510FD6A58C00E33EDE /* seqsummarycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */; };
+               379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */; };
                37AD4CE40F28AEA300AA2D49 /* sharedlistvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */; };
                37AD4DBB0F28E2FE00AA2D49 /* tree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */; };
                37AD4DCA0F28F3DD00AA2D49 /* readtree.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */; };
                37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; };
                37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.cpp */; };
+               37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73C751004BEFD008C4B41 /* listseqscommand.cpp */; };
+               37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CA51004D89A008C4B41 /* getseqscommand.cpp */; };
+               37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */; };
+               37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */; };
                37C1D9730F86506E0059E3F0 /* binsequencecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */; };
                37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37C753CD0FB3415200DBD02E /* distancecommand.cpp */; };
                37D928550F21331F001D4494 /* ace.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927B80F21331F001D4494 /* ace.cpp */; };
                37D928700F21331F001D4494 /* nameassignment.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F00F21331F001D4494 /* nameassignment.cpp */; };
                37D928720F21331F001D4494 /* npshannon.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F40F21331F001D4494 /* npshannon.cpp */; };
                37D928730F21331F001D4494 /* ordervector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F70F21331F001D4494 /* ordervector.cpp */; };
-               37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927F90F21331F001D4494 /* parselistcommand.cpp */; };
                37D928750F21331F001D4494 /* progress.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FB0F21331F001D4494 /* progress.cpp */; };
                37D928760F21331F001D4494 /* quitcommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FD0F21331F001D4494 /* quitcommand.cpp */; };
                37D928770F21331F001D4494 /* rabundvector.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927FF0F21331F001D4494 /* rabundvector.cpp */; };
                3749271C0FD58C840031C06B /* getsabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getsabundcommand.cpp; sourceTree = SOURCE_ROOT; };
                3749273D0FD5956B0031C06B /* getrabundcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getrabundcommand.h; sourceTree = SOURCE_ROOT; };
                3749273E0FD5956B0031C06B /* getrabundcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getrabundcommand.cpp; sourceTree = SOURCE_ROOT; };
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+               374F2FE9100634B600E97C66 /* bellerophon.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = bellerophon.h; sourceTree = "<group>"; };
+               374F2FEA100634B600E97C66 /* bellerophon.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = bellerophon.cpp; sourceTree = "<group>"; };
+               374F301110063B6F00E97C66 /* pintail.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = pintail.h; sourceTree = "<group>"; };
+               374F301210063B6F00E97C66 /* pintail.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = pintail.cpp; sourceTree = "<group>"; };
                37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedanderbergs.h; sourceTree = SOURCE_ROOT; };
                37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedanderbergs.cpp; sourceTree = SOURCE_ROOT; };
                37519A9F0F810D0200FED5E8 /* venncommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = venncommand.h; sourceTree = SOURCE_ROOT; };
                375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = SOURCE_ROOT; };
                375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = SOURCE_ROOT; };
                375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = SOURCE_ROOT; };
-               377326630FAF16E0007ABB8B /* concensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = concensuscommand.cpp; sourceTree = SOURCE_ROOT; };
-               377326640FAF16E0007ABB8B /* concensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = concensuscommand.h; sourceTree = SOURCE_ROOT; };
+               377326630FAF16E0007ABB8B /* consensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = consensuscommand.cpp; sourceTree = "<group>"; };
+               377326640FAF16E0007ABB8B /* consensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = consensuscommand.h; sourceTree = "<group>"; };
                378598640FDD497000EF9D03 /* heatmapsimcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsimcommand.h; sourceTree = SOURCE_ROOT; };
                378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = heatmapsimcommand.cpp; sourceTree = SOURCE_ROOT; };
                378598720FDD4C1500EF9D03 /* heatmapsim.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = heatmapsim.h; sourceTree = SOURCE_ROOT; };
                3799A94D0FD6A58C00E33EDE /* distancedb.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = distancedb.hpp; sourceTree = SOURCE_ROOT; };
                3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = seqsummarycommand.cpp; sourceTree = SOURCE_ROOT; };
                3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = seqsummarycommand.h; sourceTree = SOURCE_ROOT; };
+               379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = chimeraseqscommand.h; sourceTree = "<group>"; };
+               379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = chimeraseqscommand.cpp; sourceTree = "<group>"; };
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                37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedlistvector.h; sourceTree = SOURCE_ROOT; };
                37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedlistvector.cpp; sourceTree = SOURCE_ROOT; };
                37AD4DB90F28E2FE00AA2D49 /* tree.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = tree.h; sourceTree = SOURCE_ROOT; };
                37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedsobscollectsummary.cpp; sourceTree = SOURCE_ROOT; };
                37B28F660F27590100808A62 /* deconvolutecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = deconvolutecommand.h; sourceTree = SOURCE_ROOT; };
                37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = SOURCE_ROOT; };
+               37B73C741004BEFD008C4B41 /* listseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = listseqscommand.h; sourceTree = "<group>"; };
+               37B73C751004BEFD008C4B41 /* listseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = listseqscommand.cpp; sourceTree = "<group>"; };
+               37B73CA41004D89A008C4B41 /* getseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = getseqscommand.h; sourceTree = "<group>"; };
+               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = getseqscommand.cpp; sourceTree = "<group>"; };
+               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = removeseqscommand.h; sourceTree = "<group>"; };
+               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = removeseqscommand.cpp; sourceTree = "<group>"; };
+               37B73CCD1004F5E0008C4B41 /* systemcommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = systemcommand.h; sourceTree = "<group>"; };
+               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = systemcommand.cpp; sourceTree = "<group>"; };
                37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = SOURCE_ROOT; };
                37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = SOURCE_ROOT; };
                37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = SOURCE_ROOT; };
                37D927F60F21331F001D4494 /* observable.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = observable.h; sourceTree = SOURCE_ROOT; };
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                37D927FB0F21331F001D4494 /* progress.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = progress.cpp; sourceTree = SOURCE_ROOT; };
                37D927FC0F21331F001D4494 /* progress.hpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.h; path = progress.hpp; sourceTree = SOURCE_ROOT; };
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                                373C68DC0FC1C38D00137ACD /* blastalign.hpp */,
                                373C68DB0FC1C38D00137ACD /* blastalign.cpp */,
                                37D928A60F2133C0001D4494 /* calculators */,
+                               374F2FE81006346600E97C66 /* chimera */,
                                37D927C20F21331F001D4494 /* cluster.hpp */,
                                37D927C10F21331F001D4494 /* cluster.cpp */,
                                37D928A90F2133E5001D4494 /* commands */,
                        name = Products;
                        sourceTree = "<group>";
                };
+               374F2FE81006346600E97C66 /* chimera */ = {
+                       isa = PBXGroup;
+                       children = (
+                               374F2FD51006320200E97C66 /* chimera.h */,
+                               374F2FE9100634B600E97C66 /* bellerophon.h */,
+                               374F2FEA100634B600E97C66 /* bellerophon.cpp */,
+                               374F301110063B6F00E97C66 /* pintail.h */,
+                               374F301210063B6F00E97C66 /* pintail.cpp */,
+                       );
+                       name = chimera;
+                       sourceTree = "<group>";
+               };
                3796441D0FB9B9650081FDB6 /* read */ = {
                        isa = PBXGroup;
                        children = (
                                37C753F40FB34C0300DBD02E /* eachgapignore.h */,
                                373C69960FC1E63600137ACD /* efron.cpp */,
                                373C69970FC1E63600137ACD /* efron.h */,
+                               379D3D6B0FF917F40068C1C0 /* filters.h */,
                                EB9303F70F53517300E8EF26 /* geom.h */,
                                EB9303F80F53517300E8EF26 /* geom.cpp */,
                                378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
                                37D927C70F21331F001D4494 /* collectcommand.cpp */,
                                37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
                                37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
-                               377326640FAF16E0007ABB8B /* concensuscommand.h */,
-                               377326630FAF16E0007ABB8B /* concensuscommand.cpp */,
+                               377326640FAF16E0007ABB8B /* consensuscommand.h */,
+                               377326630FAF16E0007ABB8B /* consensuscommand.cpp */,
+                               379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */,
+                               379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */,
                                37B28F660F27590100808A62 /* deconvolutecommand.h */,
                                37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
                                37C753CC0FB3415200DBD02E /* distancecommand.h */,
                                3749273E0FD5956B0031C06B /* getrabundcommand.cpp */,
                                3749271B0FD58C840031C06B /* getsabundcommand.h */,
                                3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
+                               37B73CA41004D89A008C4B41 /* getseqscommand.h */,
+                               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
                                375873F10F7D64800040F377 /* heatmapcommand.h */,
                                375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
                                37D927E30F21331F001D4494 /* helpcommand.cpp */,
                                375873F40F7D648F0040F377 /* libshuffcommand.h */,
                                375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
+                               37B73C741004BEFD008C4B41 /* listseqscommand.h */,
+                               37B73C751004BEFD008C4B41 /* listseqscommand.cpp */,
                                21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
                                21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
                                7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
                                7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
                                375873F70F7D649C0040F377 /* nocommands.h */,
                                375873F60F7D649C0040F377 /* nocommands.cpp */,
-                               37D927FA0F21331F001D4494 /* parselistcommand.h */,
-                               37D927F90F21331F001D4494 /* parselistcommand.cpp */,
                                3792946E0F2E191800B9034A /* parsimonycommand.h */,
                                3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
                                37D927FE0F21331F001D4494 /* quitcommand.h */,
                                372E126F0F26365B0095CF7E /* readotucommand.cpp */,
                                37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
                                37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
+                               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */,
+                               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
                                7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
                                7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
                                371B30B30FD7EE67000414CA /* screenseqscommand.h */,
                                37D928460F21331F001D4494 /* summarycommand.cpp */,
                                37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
                                37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
+                               37B73CCD1004F5E0008C4B41 /* systemcommand.h */,
+                               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */,
                                211C38370F961E1F00FEE541 /* treegroupscommand.h */,
                                211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
                                7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
                                37D928700F21331F001D4494 /* nameassignment.cpp in Sources */,
                                37D928720F21331F001D4494 /* npshannon.cpp in Sources */,
                                37D928730F21331F001D4494 /* ordervector.cpp in Sources */,
-                               37D928740F21331F001D4494 /* parselistcommand.cpp in Sources */,
                                37D928750F21331F001D4494 /* progress.cpp in Sources */,
                                37D928760F21331F001D4494 /* quitcommand.cpp in Sources */,
                                37D928770F21331F001D4494 /* rabundvector.cpp in Sources */,
                                375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
                                7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */,
                                7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */,
-                               377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */,
+                               377326650FAF16E0007ABB8B /* consensuscommand.cpp in Sources */,
                                378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */,
                                378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */,
                                378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */,
                                378598740FDD4C1500EF9D03 /* heatmapsim.cpp in Sources */,
                                378599100FDD7E8E00EF9D03 /* optionparser.cpp in Sources */,
                                7E5A17AF0FE57292003C6A03 /* mergefilecommand.cpp in Sources */,
+                               379D3D510FF90E090068C1C0 /* chimeraseqscommand.cpp in Sources */,
+                               37B73C761004BEFD008C4B41 /* listseqscommand.cpp in Sources */,
+                               37B73CA61004D89A008C4B41 /* getseqscommand.cpp in Sources */,
+                               37B73CC01004EB38008C4B41 /* removeseqscommand.cpp in Sources */,
+                               37B73CCF1004F5E0008C4B41 /* systemcommand.cpp in Sources */,
+                               374F2FEB100634B600E97C66 /* bellerophon.cpp in Sources */,
+                               374F301310063B6F00E97C66 /* pintail.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };
                                );
                                GCC_OPTIMIZATION_LEVEL = 3;
                                GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
+                               GCC_WARN_ABOUT_MISSING_PROTOTYPES = YES;
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_ALLOW_INCOMPLETE_PROTOCOL = NO;
-                               GCC_WARN_PEDANTIC = NO;
+                               GCC_WARN_MISSING_PARENTHESES = YES;
+                               GCC_WARN_PEDANTIC = YES;
+                               GCC_WARN_UNUSED_FUNCTION = YES;
+                               GCC_WARN_UNUSED_PARAMETER = NO;
+                               GCC_WARN_UNUSED_VALUE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               OTHER_CPLUSPLUSFLAGS = "";
+                               OTHER_CPLUSPLUSFLAGS = (
+                                       "-ansi",
+                                       "-pedantic",
+                                       "-wall",
+                               );
                                PREBINDING = NO;
                                SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
                                WARNING_CFLAGS = "";