]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
added get.repseqs command, started matrix output command
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 1c8df765aba58235fdb4c557be80834880aa1da0..8136cc2c71aabdc3299b84edf22545ab0d095a00 100644 (file)
@@ -7,13 +7,31 @@
        objects = {
 
 /* Begin PBXBuildFile section */
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+               378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = "<group>"; };
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                EB1217220F61C9AC004A865F /* sharedkstest.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedkstest.cpp; sourceTree = "<group>"; };
                EB6E68170F5F1C780044E17B /* qstat.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = qstat.h; sourceTree = "<group>"; };
                EB6E68180F5F1C780044E17B /* qstat.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = qstat.cpp; sourceTree = "<group>"; };
-               EB6F01590F6AC1670048081A /* sharedbdiversity.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedbdiversity.h; sourceTree = "<group>"; };
-               EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedbdiversity.cpp; sourceTree = "<group>"; };
+               EB72FE240FC1F5CA0051AC11 /* shen.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = shen.cpp; sourceTree = "<group>"; };
+               EB72FE250FC1F5CA0051AC11 /* shen.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = shen.h; sourceTree = "<group>"; };
                EB9303E90F534D9400E8EF26 /* logsd.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = logsd.h; sourceTree = "<group>"; };
                EB9303EA0F534D9400E8EF26 /* logsd.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = logsd.cpp; sourceTree = "<group>"; };
                EB9303F70F53517300E8EF26 /* geom.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = geom.h; sourceTree = "<group>"; };
                08FB7795FE84155DC02AAC07 /* Source */ = {
                        isa = PBXGroup;
                        children = (
-                               7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
-                               7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
                                37D927BA0F21331F001D4494 /* averagelinkage.cpp */,
+                               373C68DC0FC1C38D00137ACD /* blastalign.hpp */,
+                               373C68DB0FC1C38D00137ACD /* blastalign.cpp */,
                                37D928A60F2133C0001D4494 /* calculators */,
                                37D927C20F21331F001D4494 /* cluster.hpp */,
                                37D927C10F21331F001D4494 /* cluster.cpp */,
-                               7E412F470F8D21B600381DD0 /* slibshuff.h */,
-                               7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
-                               7E412F420F8D213C00381DD0 /* libshuff.h */,
-                               7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
                                37D928A90F2133E5001D4494 /* commands */,
                                37D927C60F21331F001D4494 /* collect.h */,
                                37D927C50F21331F001D4494 /* collect.cpp */,
                                37D927D10F21331F001D4494 /* commandoptionparser.hpp */,
                                37D927D00F21331F001D4494 /* commandoptionparser.cpp */,
                                37D927D20F21331F001D4494 /* completelinkage.cpp */,
-                               37D927D40F21331F001D4494 /* database.hpp */,
-                               37D927D30F21331F001D4494 /* database.cpp */,
+                               7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
+                               7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
                                37D927D60F21331F001D4494 /* display.h */,
                                37D927D80F21331F001D4494 /* engine.hpp */,
                                37D927D70F21331F001D4494 /* engine.cpp */,
                                37D927DD0F21331F001D4494 /* fileoutput.cpp */,
                                37D927E00F21331F001D4494 /* globaldata.hpp */,
                                37D927DF0F21331F001D4494 /* globaldata.cpp */,
+                               373C68BB0FC1C1A600137ACD /* gotohoverlap.hpp */,
+                               373C68BA0FC1C1A600137ACD /* gotohoverlap.cpp */,
                                375873ED0F7D646F0040F377 /* heatmap.h */,
                                375873EE0F7D646F0040F377 /* heatmap.cpp */,
                                37D927E60F21331F001D4494 /* inputdata.h */,
                                37D927E50F21331F001D4494 /* inputdata.cpp */,
-                               37D927EA0F21331F001D4494 /* kmer.hpp */,
-                               37D927E90F21331F001D4494 /* kmer.cpp */,
-                               37D927EC0F21331F001D4494 /* kmerdb.hpp */,
-                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
+                               7E412F420F8D213C00381DD0 /* libshuff.h */,
+                               7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
                                37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
                                37D927F10F21331F001D4494 /* nameassignment.hpp */,
                                37D927F00F21331F001D4494 /* nameassignment.cpp */,
+                               373C691E0FC1C98600137ACD /* nast.hpp */,
+                               373C691D0FC1C98600137ACD /* nast.cpp */,
+                               373C692A0FC1C9EB00137ACD /* nastreport.hpp */,
+                               373C69290FC1C9EB00137ACD /* nastreport.cpp */,
+                               373C68CE0FC1C2D900137ACD /* needlemanoverlap.hpp */,
+                               373C68CD0FC1C2D900137ACD /* needlemanoverlap.cpp */,
+                               373C68E40FC1C4A500137ACD /* noalign.hpp */,
+                               373C68E30FC1C4A500137ACD /* noalign.cpp */,
                                37D927F60F21331F001D4494 /* observable.h */,
+                               373C68C40FC1C25F00137ACD /* overlap.hpp */,
+                               373C68C30FC1C25F00137ACD /* overlap.cpp */,
                                37D927FC0F21331F001D4494 /* progress.hpp */,
                                37D927FB0F21331F001D4494 /* progress.cpp */,
                                37D928040F21331F001D4494 /* raredisplay.h */,
                                37D928060F21331F001D4494 /* rarefact.h */,
                                37D928050F21331F001D4494 /* rarefact.cpp */,
                                37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
-                               375AA1340F9E433D008EF9B8 /* readcolumn.h */,
-                               375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
-                               37D928130F21331F001D4494 /* readmatrix.hpp */,
-                               375AA1360F9E433D008EF9B8 /* readotu.h */,
-                               375AA1350F9E433D008EF9B8 /* readotu.cpp */,
-                               375AA1380F9E433D008EF9B8 /* readphylip.h */,
-                               375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
-                               37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
-                               37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
-                               37D9281D0F21331F001D4494 /* sequence.hpp */,
-                               37D9281C0F21331F001D4494 /* sequence.cpp */,
+                               3796441D0FB9B9650081FDB6 /* read */,
                                37D928210F21331F001D4494 /* shared.h */,
                                37D928200F21331F001D4494 /* shared.cpp */,
                                211C38310F961DD400FEE541 /* sharedutilities.h */,
                                211C38300F961DD400FEE541 /* sharedutilities.cpp */,
                                37D928420F21331F001D4494 /* singlelinkage.cpp */,
+                               7E412F470F8D21B600381DD0 /* slibshuff.h */,
+                               7E412F480F8D21B600381DD0 /* slibshuff.cpp */,
                                37D928480F21331F001D4494 /* summarydata.h */,
                                37D928490F21331F001D4494 /* summarydisplay.h */,
                                37519AB30F810FAE00FED5E8 /* venn.h */,
                        name = Products;
                        sourceTree = "<group>";
                };
+               3796441D0FB9B9650081FDB6 /* read */ = {
+                       isa = PBXGroup;
+                       children = (
+                               378C1AF30FB0644D004D63F5 /* readclustal.h */,
+                               378C1AF20FB0644D004D63F5 /* readclustal.cpp */,
+                               375AA1340F9E433D008EF9B8 /* readcolumn.h */,
+                               375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
+                               378C1AF50FB0644D004D63F5 /* readfasta.h */,
+                               378C1AF40FB0644D004D63F5 /* readfasta.cpp */,
+                               37D928130F21331F001D4494 /* readmatrix.hpp */,
+                               378C1AF70FB0644D004D63F5 /* readnexus.h */,
+                               378C1AF60FB0644D004D63F5 /* readnexus.cpp */,
+                               378C1AF80FB0644D004D63F5 /* readnexusal.h */,
+                               375AA1360F9E433D008EF9B8 /* readotu.h */,
+                               375AA1350F9E433D008EF9B8 /* readotu.cpp */,
+                               375AA1380F9E433D008EF9B8 /* readphylip.h */,
+                               375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
+                               378C1AFC0FB0644D004D63F5 /* readseqsphylip.h */,
+                               378C1AFB0FB0644D004D63F5 /* readseqsphylip.cpp */,
+                               379643EB0FB9B5A80081FDB6 /* readseqs.cpp */,
+                               379643EC0FB9B5A80081FDB6 /* readseqs.h */,
+                               37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
+                               37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
+                       );
+                       name = read;
+                       sourceTree = "<group>";
+               };
                37D928A60F2133C0001D4494 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
                                37D927BE0F21331F001D4494 /* calculator.h */,
+                               373C69950FC1E63600137ACD /* boneh.h */,
+                               373C69940FC1E63600137ACD /* boneh.cpp */,
                                3792948D0F2E271100B9034A /* treecalculator.h */,
                                37D927BD0F21331F001D4494 /* calculator.cpp */,
                                37D927B90F21331F001D4494 /* ace.h */,
                                EB1216E40F61ACFB004A865F /* bstick.cpp */,
                                37D927C00F21331F001D4494 /* chao1.h */,
                                37D927BF0F21331F001D4494 /* chao1.cpp */,
+                               7EC3D4510FA0FFF900338DA5 /* coverage.h */,
+                               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
+                               37C753DF0FB3492400DBD02E /* dist.h */,
+                               37C753F00FB34AE800DBD02E /* eachgapdist.h */,
+                               37C753F40FB34C0300DBD02E /* eachgapignore.h */,
+                               373C69960FC1E63600137ACD /* efron.cpp */,
+                               373C69970FC1E63600137ACD /* efron.h */,
                                EB9303F70F53517300E8EF26 /* geom.h */,
                                EB9303F80F53517300E8EF26 /* geom.cpp */,
-                               EB9303E90F534D9400E8EF26 /* logsd.h */,
-                               EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
-                               EB6E68170F5F1C780044E17B /* qstat.h */,
-                               EB6E68180F5F1C780044E17B /* qstat.cpp */,
+                               378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
+                               378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */,
+                               37C753ED0FB34A5700DBD02E /* ignoregaps.h */,
                                37D927E80F21331F001D4494 /* jackknife.h */,
                                37D927E70F21331F001D4494 /* jackknife.cpp */,
+                               EB9303E90F534D9400E8EF26 /* logsd.h */,
+                               EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
                                375873F90F7D64AB0040F377 /* nseqs.h */,
                                37D927F50F21331F001D4494 /* npshannon.h */,
                                37D927F40F21331F001D4494 /* npshannon.cpp */,
+                               37C753F10FB34B4700DBD02E /* onegapdist.h */,
+                               37C753F30FB34BBF00DBD02E /* onegapignore.h */,
                                379294880F2E258500B9034A /* parsimony.h */,
                                379294890F2E258500B9034A /* parsimony.cpp */,
+                               EB6E68170F5F1C780044E17B /* qstat.h */,
+                               EB6E68180F5F1C780044E17B /* qstat.cpp */,
                                37D928020F21331F001D4494 /* rarecalc.h */,
                                37D928010F21331F001D4494 /* rarecalc.cpp */,
                                37D9281F0F21331F001D4494 /* shannon.h */,
                                37D928220F21331F001D4494 /* sharedace.cpp */,
                                37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
                                37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
+                               7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
                                375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
                                375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
-                               EB6F01590F6AC1670048081A /* sharedbdiversity.h */,
-                               EB6F015A0F6AC1670048081A /* sharedbdiversity.cpp */,
                                37D928250F21331F001D4494 /* sharedchao1.h */,
                                37D928240F21331F001D4494 /* sharedchao1.cpp */,
                                37D928290F21331F001D4494 /* sharedjabund.h */,
                                37D928280F21331F001D4494 /* sharedjabund.cpp */,
+                               378C1B000FB0644D004D63F5 /* sharedjackknife.h */,
+                               378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */,
                                37D9282B0F21331F001D4494 /* sharedjclass.h */,
                                37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
                                37D9282D0F21331F001D4494 /* sharedjest.h */,
                                375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
                                375874010F7D64EF0040F377 /* sharedlennon.h */,
                                375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
+                               378C1B020FB0644D004D63F5 /* sharedmarczewski.h */,
+                               378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */,
                                375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
                                375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
                                375874090F7D64FC0040F377 /* sharedochiai.h */,
                                37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
                                37D9283F0F21331F001D4494 /* sharedthetayc.h */,
                                37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
+                               EB72FE250FC1F5CA0051AC11 /* shen.h */,
+                               EB72FE240FC1F5CA0051AC11 /* shen.cpp */,
                                37D928410F21331F001D4494 /* simpson.h */,
                                37D928400F21331F001D4494 /* simpson.cpp */,
                                37D928430F21331F001D4494 /* sobs.h */,
+                               373C69980FC1E63600137ACD /* solow.cpp */,
+                               373C69990FC1E63600137ACD /* solow.h */,
                                374610810F40652400460C57 /* unweighted.h */,
                                374610820F40652400460C57 /* unweighted.cpp */,
                                37D9284E0F21331F001D4494 /* uvest.h */,
                                37D9284D0F21331F001D4494 /* uvest.cpp */,
                                3746107C0F4064D100460C57 /* weighted.h */,
                                3746107D0F4064D100460C57 /* weighted.cpp */,
+                               7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
+                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
                        );
                        name = calculators;
                        sourceTree = "<group>";
                        isa = PBXGroup;
                        children = (
                                37D927CD0F21331F001D4494 /* command.hpp */,
+                               378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
+                               378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
                                37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
                                37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
                                21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
                                37D927C70F21331F001D4494 /* collectcommand.cpp */,
                                37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
                                37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
+                               377326640FAF16E0007ABB8B /* concensuscommand.h */,
+                               377326630FAF16E0007ABB8B /* concensuscommand.cpp */,
                                37B28F660F27590100808A62 /* deconvolutecommand.h */,
                                37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
+                               37C753CC0FB3415200DBD02E /* distancecommand.h */,
+                               37C753CD0FB3415200DBD02E /* distancecommand.cpp */,
+                               378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */,
+                               378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */,
                                A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
                                A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
                                A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
                                A70B53A80F4CD7AD0064797E /* getlinecommand.cpp */,
                                370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
                                370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
+                               211A24E90FC306BC00769A33 /* getrepseqscommand.h */,
+                               211A24EA0FC306BC00769A33 /* getrepseqscommand.cpp */,
                                375873F10F7D64800040F377 /* heatmapcommand.h */,
                                375873F00F7D64800040F377 /* heatmapcommand.cpp */,
                                37D927E40F21331F001D4494 /* helpcommand.h */,
                                37D927E30F21331F001D4494 /* helpcommand.cpp */,
                                375873F40F7D648F0040F377 /* libshuffcommand.h */,
                                375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
+                               21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
+                               21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
                                375873F60F7D649C0040F377 /* nocommands.cpp */,
                                375873F70F7D649C0040F377 /* nocommands.h */,
                                37D927FA0F21331F001D4494 /* parselistcommand.h */,
                37D928AC0F213420001D4494 /* containers */ = {
                        isa = PBXGroup;
                        children = (
+                               373C68A10FC1C07D00137ACD /* alignment.hpp */,
+                               373C68A00FC1C07D00137ACD /* alignment.cpp */,
+                               373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
+                               373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
+                               373C69170FC1C8AF00137ACD /* blastdb.hpp */,
+                               373C69160FC1C8AF00137ACD /* blastdb.cpp */,
+                               37D927D40F21331F001D4494 /* database.hpp */,
+                               37D927D30F21331F001D4494 /* database.cpp */,
                                37D927D50F21331F001D4494 /* datavector.hpp */,
                                37D927DC0F21331F001D4494 /* fastamap.h */,
                                37D927DB0F21331F001D4494 /* fastamap.cpp */,
                                375873EB0F7D64520040F377 /* fullmatrix.cpp */,
                                37D927E20F21331F001D4494 /* groupmap.h */,
                                37D927E10F21331F001D4494 /* groupmap.cpp */,
+                               37D927EA0F21331F001D4494 /* kmer.hpp */,
+                               37D927E90F21331F001D4494 /* kmer.cpp */,
+                               37D927EC0F21331F001D4494 /* kmerdb.hpp */,
+                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
                                37D927EE0F21331F001D4494 /* listvector.hpp */,
                                37D927ED0F21331F001D4494 /* listvector.cpp */,
                                37D927F80F21331F001D4494 /* ordervector.hpp */,
                                37D927FF0F21331F001D4494 /* rabundvector.cpp */,
                                37D9281B0F21331F001D4494 /* sabundvector.hpp */,
                                37D9281A0F21331F001D4494 /* sabundvector.cpp */,
+                               37D9281D0F21331F001D4494 /* sequence.hpp */,
+                               37D9281C0F21331F001D4494 /* sequence.cpp */,
+                               378C1AFE0FB0644D004D63F5 /* sequencedb.h */,
+                               378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */,
                                37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
                                37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
                                37D9282F0F21331F001D4494 /* sharedordervector.h */,
                                37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
                                37D928450F21331F001D4494 /* sparsematrix.hpp */,
                                37D928440F21331F001D4494 /* sparsematrix.cpp */,
+                               373C68F40FC1C6A800137ACD /* suffixdb.hpp */,
+                               373C68F30FC1C6A800137ACD /* suffixdb.cpp */,
+                               373C68F60FC1C6A800137ACD /* suffixnodes.hpp */,
+                               373C68F50FC1C6A800137ACD /* suffixnodes.cpp */,
+                               373C68F80FC1C6A800137ACD /* suffixtree.hpp */,
+                               373C68F70FC1C6A800137ACD /* suffixtree.cpp */,
                                37AD4DB90F28E2FE00AA2D49 /* tree.h */,
                                37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
                                379293C10F2DE73400B9034A /* treemap.h */,
                                EB1216880F619B83004A865F /* bergerparker.cpp in Sources */,
                                EB1216E50F61ACFB004A865F /* bstick.cpp in Sources */,
                                EB1217230F61C9AC004A865F /* sharedkstest.cpp in Sources */,
-                               EB6F015B0F6AC1670048081A /* sharedbdiversity.cpp in Sources */,
                                375873EC0F7D64520040F377 /* fullmatrix.cpp in Sources */,
                                375873EF0F7D646F0040F377 /* heatmap.cpp in Sources */,
                                375873F20F7D64800040F377 /* heatmapcommand.cpp in Sources */,
                                375AA1390F9E433D008EF9B8 /* readcolumn.cpp in Sources */,
                                375AA13A0F9E433D008EF9B8 /* readotu.cpp in Sources */,
                                375AA13B0F9E433D008EF9B8 /* readphylip.cpp in Sources */,
+                               7EC3D4550FA0FFF900338DA5 /* coverage.cpp in Sources */,
+                               7EC3D4560FA0FFF900338DA5 /* whittaker.cpp in Sources */,
+                               377326650FAF16E0007ABB8B /* concensuscommand.cpp in Sources */,
+                               378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */,
+                               378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */,
+                               378C1B050FB0644E004D63F5 /* readclustal.cpp in Sources */,
+                               378C1B060FB0644E004D63F5 /* readfasta.cpp in Sources */,
+                               378C1B070FB0644E004D63F5 /* readnexus.cpp in Sources */,
+                               378C1B090FB0644E004D63F5 /* readseqsphylip.cpp in Sources */,
+                               378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */,
+                               378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */,
+                               378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */,
+                               37C753CE0FB3415200DBD02E /* distancecommand.cpp in Sources */,
+                               379643ED0FB9B5A80081FDB6 /* readseqs.cpp in Sources */,
+                               378DC5CF0FBDE1C8003B8607 /* aligncommand.cpp in Sources */,
+                               373C68A40FC1C07D00137ACD /* alignment.cpp in Sources */,
+                               373C68A50FC1C07D00137ACD /* alignmentcell.cpp in Sources */,
+                               373C68BC0FC1C1A600137ACD /* gotohoverlap.cpp in Sources */,
+                               373C68C50FC1C25F00137ACD /* overlap.cpp in Sources */,
+                               373C68CF0FC1C2D900137ACD /* needlemanoverlap.cpp in Sources */,
+                               373C68DD0FC1C38D00137ACD /* blastalign.cpp in Sources */,
+                               373C68E50FC1C4A500137ACD /* noalign.cpp in Sources */,
+                               373C68F90FC1C6A800137ACD /* suffixdb.cpp in Sources */,
+                               373C68FA0FC1C6A800137ACD /* suffixnodes.cpp in Sources */,
+                               373C68FB0FC1C6A800137ACD /* suffixtree.cpp in Sources */,
+                               373C69180FC1C8AF00137ACD /* blastdb.cpp in Sources */,
+                               373C691F0FC1C98600137ACD /* nast.cpp in Sources */,
+                               373C692B0FC1C9EB00137ACD /* nastreport.cpp in Sources */,
+                               373C699A0FC1E63600137ACD /* boneh.cpp in Sources */,
+                               373C699B0FC1E63600137ACD /* efron.cpp in Sources */,
+                               373C699C0FC1E63600137ACD /* solow.cpp in Sources */,
+                               EB72FE260FC1F5CA0051AC11 /* shen.cpp in Sources */,
+                               211A24EB0FC306BC00769A33 /* getrepseqscommand.cpp in Sources */,
+                               21E859D80FC4632E005E1A48 /* matrixoutputcommand.cpp in Sources */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };