]> git.donarmstrong.com Git - mothur.git/blobdiff - Mothur.xcodeproj/project.pbxproj
altered venn command to make use of sharedchao for any number of groups, fixed window...
[mothur.git] / Mothur.xcodeproj / project.pbxproj
index 7da4ca2f32624a87b9932907fe44a02c1eb6acb8..d29d52e10c177f12f9721223058495cfd28fffde 100644 (file)
                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 */; };
+               378C1B030FB0644E004D63F5 /* filterseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */; };
+               378C1B040FB0644E004D63F5 /* goodscoverage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */; };
+               378C1B050FB0644E004D63F5 /* readclustal.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF20FB0644D004D63F5 /* readclustal.cpp */; };
+               378C1B060FB0644E004D63F5 /* readfasta.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF40FB0644D004D63F5 /* readfasta.cpp */; };
+               378C1B070FB0644E004D63F5 /* readnexus.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF60FB0644D004D63F5 /* readnexus.cpp */; };
+               378C1B080FB0644E004D63F5 /* readseqscommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AF90FB0644D004D63F5 /* readseqscommand.cpp */; };
+               378C1B090FB0644E004D63F5 /* readseqsphylip.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFB0FB0644D004D63F5 /* readseqsphylip.cpp */; };
+               378C1B0A0FB0644E004D63F5 /* sequencedb.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */; };
+               378C1B0B0FB0644E004D63F5 /* sharedjackknife.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */; };
+               378C1B0C0FB0644E004D63F5 /* sharedmarczewski.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */; };
                379293C30F2DE73400B9034A /* treemap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379293C20F2DE73400B9034A /* treemap.cpp */; };
                379294700F2E191800B9034A /* parsimonycommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 3792946F0F2E191800B9034A /* parsimonycommand.cpp */; };
                3792948A0F2E258500B9034A /* parsimony.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 379294890F2E258500B9034A /* parsimony.cpp */; };
@@ -45,6 +55,7 @@
                37AFC71F0F445386005F492D /* sharedsobscollectsummary.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */; };
                37B28F680F27590100808A62 /* deconvolutecommand.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37B28F670F27590100808A62 /* deconvolutecommand.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 */; };
                37D928560F21331F001D4494 /* averagelinkage.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BA0F21331F001D4494 /* averagelinkage.cpp */; };
                37D928570F21331F001D4494 /* bootstrap.cpp in Sources */ = {isa = PBXBuildFile; fileRef = 37D927BB0F21331F001D4494 /* bootstrap.cpp */; };
                375AA1360F9E433D008EF9B8 /* readotu.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readotu.h; sourceTree = "<group>"; };
                375AA1370F9E433D008EF9B8 /* readphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readphylip.cpp; sourceTree = "<group>"; };
                375AA1380F9E433D008EF9B8 /* readphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readphylip.h; sourceTree = "<group>"; };
-               377326560FAF16DF007ABB8B /* categories.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = categories.pbxbtree; sourceTree = "<group>"; };
-               377326570FAF16DF007ABB8B /* cdecls.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = cdecls.pbxbtree; sourceTree = "<group>"; };
-               377326580FAF16DF007ABB8B /* decls.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = decls.pbxbtree; sourceTree = "<group>"; };
-               377326590FAF16DF007ABB8B /* files.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = files.pbxbtree; sourceTree = "<group>"; };
-               3773265A0FAF16DF007ABB8B /* imports.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = imports.pbxbtree; sourceTree = "<group>"; };
-               3773265B0FAF16DF007ABB8B /* pbxindex.header */ = {isa = PBXFileReference; lastKnownFileType = file; path = pbxindex.header; sourceTree = "<group>"; };
-               3773265C0FAF16DF007ABB8B /* protocols.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = protocols.pbxbtree; sourceTree = "<group>"; };
-               3773265D0FAF16DF007ABB8B /* refs.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = refs.pbxbtree; sourceTree = "<group>"; };
-               3773265F0FAF16DF007ABB8B /* control */ = {isa = PBXFileReference; lastKnownFileType = file; path = control; sourceTree = "<group>"; };
-               377326600FAF16DF007ABB8B /* strings */ = {isa = PBXFileReference; lastKnownFileType = file; path = strings; sourceTree = "<group>"; };
-               377326610FAF16E0007ABB8B /* subclasses.pbxbtree */ = {isa = PBXFileReference; lastKnownFileType = file; path = subclasses.pbxbtree; sourceTree = "<group>"; };
-               377326620FAF16E0007ABB8B /* symbols0.pbxsymbols */ = {isa = PBXFileReference; lastKnownFileType = file; path = symbols0.pbxsymbols; sourceTree = "<group>"; };
                377326630FAF16E0007ABB8B /* concensuscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = concensuscommand.cpp; sourceTree = "<group>"; };
                377326640FAF16E0007ABB8B /* concensuscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = concensuscommand.h; sourceTree = "<group>"; };
+               378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = filterseqscommand.cpp; sourceTree = "<group>"; };
+               378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = filterseqscommand.h; sourceTree = "<group>"; };
+               378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = goodscoverage.cpp; sourceTree = "<group>"; };
+               378C1AF10FB0644D004D63F5 /* goodscoverage.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = goodscoverage.h; sourceTree = "<group>"; };
+               378C1AF20FB0644D004D63F5 /* readclustal.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readclustal.cpp; sourceTree = "<group>"; };
+               378C1AF30FB0644D004D63F5 /* readclustal.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readclustal.h; sourceTree = "<group>"; };
+               378C1AF40FB0644D004D63F5 /* readfasta.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readfasta.cpp; sourceTree = "<group>"; };
+               378C1AF50FB0644D004D63F5 /* readfasta.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readfasta.h; sourceTree = "<group>"; };
+               378C1AF60FB0644D004D63F5 /* readnexus.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readnexus.cpp; sourceTree = "<group>"; };
+               378C1AF70FB0644D004D63F5 /* readnexus.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readnexus.h; sourceTree = "<group>"; };
+               378C1AF80FB0644D004D63F5 /* readnexusal.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readnexusal.h; sourceTree = "<group>"; };
+               378C1AF90FB0644D004D63F5 /* readseqscommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readseqscommand.cpp; sourceTree = "<group>"; };
+               378C1AFA0FB0644D004D63F5 /* readseqscommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readseqscommand.h; sourceTree = "<group>"; };
+               378C1AFB0FB0644D004D63F5 /* readseqsphylip.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = readseqsphylip.cpp; sourceTree = "<group>"; };
+               378C1AFC0FB0644D004D63F5 /* readseqsphylip.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = readseqsphylip.h; sourceTree = "<group>"; };
+               378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sequencedb.cpp; sourceTree = "<group>"; };
+               378C1AFE0FB0644D004D63F5 /* sequencedb.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sequencedb.h; sourceTree = "<group>"; };
+               378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedjackknife.cpp; sourceTree = "<group>"; };
+               378C1B000FB0644D004D63F5 /* sharedjackknife.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedjackknife.h; sourceTree = "<group>"; };
+               378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = sharedmarczewski.cpp; sourceTree = "<group>"; };
+               378C1B020FB0644D004D63F5 /* sharedmarczewski.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = sharedmarczewski.h; sourceTree = "<group>"; };
                379293C10F2DE73400B9034A /* treemap.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = treemap.h; sourceTree = "<group>"; };
                379293C20F2DE73400B9034A /* treemap.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = treemap.cpp; sourceTree = "<group>"; };
                3792946E0F2E191800B9034A /* parsimonycommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = parsimonycommand.h; sourceTree = "<group>"; };
                37B28F670F27590100808A62 /* deconvolutecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = deconvolutecommand.cpp; sourceTree = "<group>"; };
                37C1D9710F86506E0059E3F0 /* binsequencecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = binsequencecommand.h; sourceTree = "<group>"; };
                37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = binsequencecommand.cpp; sourceTree = "<group>"; };
+               37C753CC0FB3415200DBD02E /* distancecommand.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = distancecommand.h; sourceTree = "<group>"; };
+               37C753CD0FB3415200DBD02E /* distancecommand.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = distancecommand.cpp; sourceTree = "<group>"; };
+               37C753DF0FB3492400DBD02E /* dist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = dist.h; sourceTree = "<group>"; };
+               37C753ED0FB34A5700DBD02E /* ignoregaps.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ignoregaps.h; sourceTree = "<group>"; };
+               37C753F00FB34AE800DBD02E /* eachgapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapdist.h; sourceTree = "<group>"; };
+               37C753F10FB34B4700DBD02E /* onegapdist.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapdist.h; sourceTree = "<group>"; };
+               37C753F30FB34BBF00DBD02E /* onegapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = onegapignore.h; sourceTree = "<group>"; };
+               37C753F40FB34C0300DBD02E /* eachgapignore.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = eachgapignore.h; sourceTree = "<group>"; };
                37D927B80F21331F001D4494 /* ace.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = ace.cpp; sourceTree = "<group>"; };
                37D927B90F21331F001D4494 /* ace.h */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.c.h; path = ace.h; sourceTree = "<group>"; };
                37D927BA0F21331F001D4494 /* averagelinkage.cpp */ = {isa = PBXFileReference; fileEncoding = 4; lastKnownFileType = sourcecode.cpp.cpp; path = averagelinkage.cpp; sourceTree = "<group>"; };
                08FB7794FE84155DC02AAC07 /* Mothur */ = {
                        isa = PBXGroup;
                        children = (
-                               377326530FAF16DF007ABB8B /* build */,
                                08FB7795FE84155DC02AAC07 /* Source */,
                                C6859E8C029090F304C91782 /* Documentation */,
                                1AB674ADFE9D54B511CA2CBB /* Products */,
                08FB7795FE84155DC02AAC07 /* Source */ = {
                        isa = PBXGroup;
                        children = (
-                               7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
-                               7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
                                37D927BA0F21331F001D4494 /* averagelinkage.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 */,
                                37D927D20F21331F001D4494 /* completelinkage.cpp */,
                                37D927D40F21331F001D4494 /* database.hpp */,
                                37D927D30F21331F001D4494 /* database.cpp */,
+                               7E4130F70F8E58FA00381DD0 /* dlibshuff.h */,
+                               7E4130F60F8E58FA00381DD0 /* dlibshuff.cpp */,
                                37D927D60F21331F001D4494 /* display.h */,
+                               37C753DF0FB3492400DBD02E /* dist.h */,
                                37D927D80F21331F001D4494 /* engine.hpp */,
                                37D927D70F21331F001D4494 /* engine.cpp */,
                                37D928B10F213472001D4494 /* errorcheckor */,
                                37D927E90F21331F001D4494 /* kmer.cpp */,
                                37D927EC0F21331F001D4494 /* kmerdb.hpp */,
                                37D927EB0F21331F001D4494 /* kmerdb.cpp */,
+                               7E412F420F8D213C00381DD0 /* libshuff.h */,
+                               7E412FE90F8D3E2C00381DD0 /* libshuff.cpp */,
                                37E3ED800F4D9D0D00B5DF02 /* mothur.h */,
                                37D927EF0F21331F001D4494 /* mothur.cpp */,
                                37D927F10F21331F001D4494 /* nameassignment.hpp */,
                                37D928060F21331F001D4494 /* rarefact.h */,
                                37D928050F21331F001D4494 /* rarefact.cpp */,
                                37D928090F21331F001D4494 /* rarefactioncurvedata.h */,
+                               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 */,
                                37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
                                37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
-                               37D9281D0F21331F001D4494 /* sequence.hpp */,
-                               37D9281C0F21331F001D4494 /* sequence.cpp */,
                                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>";
                };
-               377326530FAF16DF007ABB8B /* build */ = {
-                       isa = PBXGroup;
-                       children = (
-                               377326540FAF16DF007ABB8B /* Mothur.build */,
-                       );
-                       path = build;
-                       sourceTree = "<group>";
-               };
-               377326540FAF16DF007ABB8B /* Mothur.build */ = {
-                       isa = PBXGroup;
-                       children = (
-                               377326550FAF16DF007ABB8B /* Mothur.pbxindex */,
-                       );
-                       path = Mothur.build;
-                       sourceTree = "<group>";
-               };
-               377326550FAF16DF007ABB8B /* Mothur.pbxindex */ = {
-                       isa = PBXGroup;
-                       children = (
-                               377326560FAF16DF007ABB8B /* categories.pbxbtree */,
-                               377326570FAF16DF007ABB8B /* cdecls.pbxbtree */,
-                               377326580FAF16DF007ABB8B /* decls.pbxbtree */,
-                               377326590FAF16DF007ABB8B /* files.pbxbtree */,
-                               3773265A0FAF16DF007ABB8B /* imports.pbxbtree */,
-                               3773265B0FAF16DF007ABB8B /* pbxindex.header */,
-                               3773265C0FAF16DF007ABB8B /* protocols.pbxbtree */,
-                               3773265D0FAF16DF007ABB8B /* refs.pbxbtree */,
-                               3773265E0FAF16DF007ABB8B /* strings.pbxstrings */,
-                               377326610FAF16E0007ABB8B /* subclasses.pbxbtree */,
-                               377326620FAF16E0007ABB8B /* symbols0.pbxsymbols */,
-                       );
-                       path = Mothur.pbxindex;
-                       sourceTree = "<group>";
-               };
-               3773265E0FAF16DF007ABB8B /* strings.pbxstrings */ = {
-                       isa = PBXGroup;
-                       children = (
-                               3773265F0FAF16DF007ABB8B /* control */,
-                               377326600FAF16DF007ABB8B /* strings */,
-                       );
-                       path = strings.pbxstrings;
-                       sourceTree = "<group>";
-               };
                37D928A60F2133C0001D4494 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
                                EB1216E40F61ACFB004A865F /* bstick.cpp */,
                                37D927C00F21331F001D4494 /* chao1.h */,
                                37D927BF0F21331F001D4494 /* chao1.cpp */,
+                               7EC3D4510FA0FFF900338DA5 /* coverage.h */,
+                               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
+                               37C753F00FB34AE800DBD02E /* eachgapdist.h */,
+                               37C753F40FB34C0300DBD02E /* eachgapignore.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 */,
-                               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
-                               7EC3D4510FA0FFF900338DA5 /* coverage.h */,
                                7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
-                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
-                               7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
                                375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
                                375873FC0F7D64DA0040F377 /* sharedbraycurtis.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 */,
                                37D9284D0F21331F001D4494 /* uvest.cpp */,
                                3746107C0F4064D100460C57 /* weighted.h */,
                                3746107D0F4064D100460C57 /* weighted.cpp */,
+                               7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
+                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
                        );
                        name = calculators;
                        sourceTree = "<group>";
                                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 */,
                                372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
                                372E126E0F26365B0095CF7E /* readotucommand.h */,
                                372E126F0F26365B0095CF7E /* readotucommand.cpp */,
+                               378C1AFA0FB0644D004D63F5 /* readseqscommand.h */,
+                               378C1AF90FB0644D004D63F5 /* readseqscommand.cpp */,
                                37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
                                37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
                                37D928270F21331F001D4494 /* sharedcommand.h */,
                                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 */,
                                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 */,
+                               378C1B080FB0644E004D63F5 /* readseqscommand.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 */,
                        );
                        runOnlyForDeploymentPostprocessing = 0;
                };