Changed back to xcode build.

diff --git a/Mothur.1 b/Mothur.1
index 42e748ce16af913c6034f07c00dc680af8c0dd7f..e8070f814216fbe17171c9dcd09f9376ad7247ca 100644 (file)
--- a/Mothur.1
+++ b/Mothur.1
@@ -1,79 +1,79 @@
-.\"Modified from man(1) of FreeBSD, the NetBSD mdoc.template, and mdoc.samples.\r
-.\"See Also:\r
-.\"man mdoc.samples for a complete listing of options\r
-.\"man mdoc for the short list of editing options\r
-.\"/usr/share/misc/mdoc.template\r
-.Dd 1/16/09               \" DATE \r
-.Dt Mothur 1      \" Program name and manual section number \r
-.Os Darwin\r
-.Sh NAME                 \" Section Header - required - don't modify \r
-.Nm Mothur,\r
-.\" The following lines are read in generating the apropos(man -k) database. Use only key\r
-.\" words here as the database is built based on the words here and in the .ND line. \r
-.Nm Other_name_for_same_program(),\r
-.Nm Yet another name for the same program.\r
-.\" Use .Nm macro to designate other names for the documented program.\r
-.Nd This line parsed for whatis database.\r
-.Sh SYNOPSIS             \" Section Header - required - don't modify\r
-.Nm\r
-.Op Fl abcd              \" [-abcd]\r
-.Op Fl a Ar path         \" [-a path] \r
-.Op Ar file              \" [file]\r
-.Op Ar                   \" [file ...]\r
-.Ar arg0                 \" Underlined argument - use .Ar anywhere to underline\r
-arg2 ...                 \" Arguments\r
-.Sh DESCRIPTION          \" Section Header - required - don't modify\r
-Use the .Nm macro to refer to your program throughout the man page like such:\r
-.Nm\r
-Underlining is accomplished with the .Ar macro like this:\r
-.Ar underlined text .\r
-.Pp                      \" Inserts a space\r
-A list of items with descriptions:\r
-.Bl -tag -width -indent  \" Begins a tagged list \r
-.It item a               \" Each item preceded by .It macro\r
-Description of item a\r
-.It item b\r
-Description of item b\r
-.El                      \" Ends the list\r
-.Pp\r
-A list of flags and their descriptions:\r
-.Bl -tag -width -indent  \" Differs from above in tag removed \r
-.It Fl a                 \"-a flag as a list item\r
-Description of -a flag\r
-.It Fl b\r
-Description of -b flag\r
-.El                      \" Ends the list\r
-.Pp\r
-.\" .Sh ENVIRONMENT      \" May not be needed\r
-.\" .Bl -tag -width "ENV_VAR_1" -indent \" ENV_VAR_1 is width of the string ENV_VAR_1\r
-.\" .It Ev ENV_VAR_1\r
-.\" Description of ENV_VAR_1\r
-.\" .It Ev ENV_VAR_2\r
-.\" Description of ENV_VAR_2\r
-.\" .El                      \r
-.Sh FILES                \" File used or created by the topic of the man page\r
-.Bl -tag -width "/Users/joeuser/Library/really_long_file_name" -compact\r
-.It Pa /usr/share/file_name\r
-FILE_1 description\r
-.It Pa /Users/joeuser/Library/really_long_file_name\r
-FILE_2 description\r
-.El                      \" Ends the list\r
-.\" .Sh DIAGNOSTICS       \" May not be needed\r
-.\" .Bl -diag\r
-.\" .It Diagnostic Tag\r
-.\" Diagnostic informtion here.\r
-.\" .It Diagnostic Tag\r
-.\" Diagnostic informtion here.\r
-.\" .El\r
-.Sh SEE ALSO \r
-.\" List links in ascending order by section, alphabetically within a section.\r
-.\" Please do not reference files that do not exist without filing a bug report\r
-.Xr a 1 , \r
-.Xr b 1 ,\r
-.Xr c 1 ,\r
-.Xr a 2 ,\r
-.Xr b 2 ,\r
-.Xr a 3 ,\r
-.Xr b 3 \r
-.\" .Sh BUGS              \" Document known, unremedied bugs \r
-.\" .Sh HISTORY           \" Document history if command behaves in a unique manner 
\ No newline at end of file
+.\"Modified from man(1) of FreeBSD, the NetBSD mdoc.template, and mdoc.samples.
+.\"See Also:
+.\"man mdoc.samples for a complete listing of options
+.\"man mdoc for the short list of editing options
+.\"/usr/share/misc/mdoc.template
+.Dd 1/4/11               \" DATE 
+.Dt mothur 1      \" Program name and manual section number 
+.Os Darwin
+.Sh NAME                 \" Section Header - required - don't modify 
+.Nm mothur,
+.\" The following lines are read in generating the apropos(man -k) database. Use only key
+.\" words here as the database is built based on the words here and in the .ND line. 
+.Nm Other_name_for_same_program(),
+.Nm Yet another name for the same program.
+.\" Use .Nm macro to designate other names for the documented program.
+.Nd This line parsed for whatis database.
+.Sh SYNOPSIS             \" Section Header - required - don't modify
+.Nm
+.Op Fl abcd              \" [-abcd]
+.Op Fl a Ar path         \" [-a path] 
+.Op Ar file              \" [file]
+.Op Ar                   \" [file ...]
+.Ar arg0                 \" Underlined argument - use .Ar anywhere to underline
+arg2 ...                 \" Arguments
+.Sh DESCRIPTION          \" Section Header - required - don't modify
+Use the .Nm macro to refer to your program throughout the man page like such:
+.Nm
+Underlining is accomplished with the .Ar macro like this:
+.Ar underlined text .
+.Pp                      \" Inserts a space
+A list of items with descriptions:
+.Bl -tag -width -indent  \" Begins a tagged list 
+.It item a               \" Each item preceded by .It macro
+Description of item a
+.It item b
+Description of item b
+.El                      \" Ends the list
+.Pp
+A list of flags and their descriptions:
+.Bl -tag -width -indent  \" Differs from above in tag removed 
+.It Fl a                 \"-a flag as a list item
+Description of -a flag
+.It Fl b
+Description of -b flag
+.El                      \" Ends the list
+.Pp
+.\" .Sh ENVIRONMENT      \" May not be needed
+.\" .Bl -tag -width "ENV_VAR_1" -indent \" ENV_VAR_1 is width of the string ENV_VAR_1
+.\" .It Ev ENV_VAR_1
+.\" Description of ENV_VAR_1
+.\" .It Ev ENV_VAR_2
+.\" Description of ENV_VAR_2
+.\" .El                      
+.Sh FILES                \" File used or created by the topic of the man page
+.Bl -tag -width "/Users/joeuser/Library/really_long_file_name" -compact
+.It Pa /usr/share/file_name
+FILE_1 description
+.It Pa /Users/joeuser/Library/really_long_file_name
+FILE_2 description
+.El                      \" Ends the list
+.\" .Sh DIAGNOSTICS       \" May not be needed
+.\" .Bl -diag
+.\" .It Diagnostic Tag
+.\" Diagnostic informtion here.
+.\" .It Diagnostic Tag
+.\" Diagnostic informtion here.
+.\" .El
+.Sh SEE ALSO 
+.\" List links in ascending order by section, alphabetically within a section.
+.\" Please do not reference files that do not exist without filing a bug report
+.Xr a 1 , 
+.Xr b 1 ,
+.Xr c 1 ,
+.Xr a 2 ,
+.Xr b 2 ,
+.Xr a 3 ,
+.Xr b 3 
+.\" .Sh BUGS              \" Document known, unremedied bugs 
+.\" .Sh HISTORY           \" Document history if command behaves in a unique manner
\ No newline at end of file

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index edb26d37714cb4702183fc00dc182ba632f15506..34bc7d9f0cd60ae34f4ba5c6831f78cf5b32851b 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -3,1239 +3,1562 @@
        archiveVersion = 1;
        classes = {
        };
-       objectVersion = 44;
+       objectVersion = 45;
        objects = {
 
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-                               A7DA2115113FECD400BF472F /* sharedjclass.cpp */,
-                               A7DA2116113FECD400BF472F /* sharedjclass.h */,
-                               A7DA2117113FECD400BF472F /* sharedjest.cpp */,
-                               A7DA2118113FECD400BF472F /* sharedjest.h */,
-                               A7DA2119113FECD400BF472F /* sharedkstest.cpp */,
-                               A7DA211A113FECD400BF472F /* sharedkstest.h */,
-                               A7DA211B113FECD400BF472F /* sharedkulczynski.cpp */,
-                               A7DA211C113FECD400BF472F /* sharedkulczynski.h */,
-                               A7DA211D113FECD400BF472F /* sharedkulczynskicody.cpp */,
-                               A7DA211E113FECD400BF472F /* sharedkulczynskicody.h */,
-                               A7DA211F113FECD400BF472F /* sharedlennon.cpp */,
-                               A7DA2120113FECD400BF472F /* sharedlennon.h */,
-                               A7DA2123113FECD400BF472F /* sharedmarczewski.cpp */,
-                               A7DA2124113FECD400BF472F /* sharedmarczewski.h */,
-                               A7DA2125113FECD400BF472F /* sharedmorisitahorn.cpp */,
-                               A7DA2126113FECD400BF472F /* sharedmorisitahorn.h */,
-                               A7DA2127113FECD400BF472F /* sharednseqs.h */,
-                               A7DA2128113FECD400BF472F /* sharedochiai.cpp */,
-                               A7DA2129113FECD400BF472F /* sharedochiai.h */,
-                               A7DA2130113FECD400BF472F /* sharedsobs.cpp */,
-                               A7DA2131113FECD400BF472F /* sharedsobs.h */,
-                               A7DA2132113FECD400BF472F /* sharedsobscollectsummary.cpp */,
-                               A7DA2133113FECD400BF472F /* sharedsobscollectsummary.h */,
-                               A7DA2134113FECD400BF472F /* sharedsorabund.cpp */,
-                               A7DA2135113FECD400BF472F /* sharedsorabund.h */,
-                               A7DA2136113FECD400BF472F /* sharedsorclass.cpp */,
-                               A7DA2137113FECD400BF472F /* sharedsorclass.h */,
-                               A7DA2138113FECD400BF472F /* sharedsorest.cpp */,
-                               A7DA2139113FECD400BF472F /* sharedsorest.h */,
-                               A7DA213A113FECD400BF472F /* sharedthetan.cpp */,
-                               A7DA213B113FECD400BF472F /* sharedthetan.h */,
-                               A7DA213C113FECD400BF472F /* sharedthetayc.cpp */,
-                               A7DA213D113FECD400BF472F /* sharedthetayc.h */,
-                               A7DA2140113FECD400BF472F /* shen.cpp */,
-                               A7DA2141113FECD400BF472F /* shen.h */,
-                               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 */,
-                               A7DA216F113FECD400BF472F /* uvest.cpp */,
-                               A7DA2170113FECD400BF472F /* uvest.h */,
-                               A7DA2179113FECD400BF472F /* weighted.cpp */,
-                               A7DA217A113FECD400BF472F /* weighted.h */,
-                               7EC61A0911BEA6AF00F668D9 /* weightedlinkage.cpp */,
-                               A7DA217B113FECD400BF472F /* whittaker.cpp */,
-                               A7DA217C113FECD400BF472F /* whittaker.h */,
+                               A7E9B65912D37EC300DA6239 /* averagelinkage.cpp */,
+                               A7E9BA4F12D398D700DA6239 /* clearcut */,
+                               A7E9B69812D37EC400DA6239 /* cluster.cpp */,
+                               A7E9B69912D37EC400DA6239 /* cluster.hpp */,
+                               A7E9B69A12D37EC400DA6239 /* clusterclassic.cpp */,
+                               A7E9B69B12D37EC400DA6239 /* clusterclassic.h */,
+                               A7E9BA3F12D395F700DA6239 /* calculators */,
+                               A7E9BA4512D3965600DA6239 /* chimera */,
+                               A7E9BA4B12D3966900DA6239 /* classifier */,
+                               A7E9B6A612D37EC400DA6239 /* collect.cpp */,
+                               A7E9B6A712D37EC400DA6239 /* collect.h */,
+                               A7E9B6AA12D37EC400DA6239 /* collectdisplay.h */,
+                               A7E9B6AB12D37EC400DA6239 /* collectorscurvedata.h */,
+                               A7E9BA3812D3956100DA6239 /* commands */,
+                               A7E9B6AF12D37EC400DA6239 /* commandfactory.cpp */,
+                               A7E9B6B012D37EC400DA6239 /* commandfactory.hpp */,
+                               A7E9B6B112D37EC400DA6239 /* commandoptionparser.cpp */,
+                               A7E9B6B212D37EC400DA6239 /* commandoptionparser.hpp */,
+                               A7E9B6B412D37EC400DA6239 /* completelinkage.cpp */,
+                               A7E9BA4212D3960D00DA6239 /* containers */,
+                               A7E9B6C912D37EC400DA6239 /* display.h */,
+                               A7E9B6D112D37EC400DA6239 /* dlibshuff.cpp */,
+                               A7E9B6D212D37EC400DA6239 /* dlibshuff.h */,
+                               A7E9B6D912D37EC400DA6239 /* endiannessmacros.h */,
+                               A7E9B6DA12D37EC400DA6239 /* engine.cpp */,
+                               A7E9B6DB12D37EC400DA6239 /* engine.hpp */,
+                               A7E9B6E012D37EC400DA6239 /* fileoutput.cpp */,
+                               A7E9B6E112D37EC400DA6239 /* fileoutput.h */,
+                               A7E9B70C12D37EC400DA6239 /* globaldata.cpp */,
+                               A7E9B70D12D37EC400DA6239 /* globaldata.hpp */,
+                               A7E9B71112D37EC400DA6239 /* gotohoverlap.hpp */,
+                               A7E9B71012D37EC400DA6239 /* gotohoverlap.cpp */,
+                               A7E9B71812D37EC400DA6239 /* hcluster.cpp */,
+                               A7E9B71912D37EC400DA6239 /* hcluster.h */,
+                               A7E9B71C12D37EC400DA6239 /* heatmap.cpp */,
+                               A7E9B71D12D37EC400DA6239 /* heatmap.h */,
+                               A7E9B72012D37EC400DA6239 /* heatmapsim.cpp */,
+                               A7E9B72112D37EC400DA6239 /* heatmapsim.h */,
+                               A7E9B72E12D37EC400DA6239 /* inputdata.h */,
+                               A7E9B72D12D37EC400DA6239 /* inputdata.cpp */,
+                               A7E9B73912D37EC400DA6239 /* libshuff.cpp */,
+                               A7E9B73A12D37EC400DA6239 /* libshuff.h */,
+                               A7E9BA5612D39BD800DA6239 /* metastats */,
+                               A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
+                               A7E9B75C12D37EC400DA6239 /* mothur.h */,
+                               A7E9B75D12D37EC400DA6239 /* mothurout.cpp */,
+                               A7E9B75E12D37EC400DA6239 /* mothurout.h */,
+                               A7E9B76512D37EC400DA6239 /* needlemanoverlap.cpp */,
+                               A7E9B76612D37EC400DA6239 /* needlemanoverlap.hpp */,
+                               A7E9B77012D37EC400DA6239 /* observable.h */,
+                               A7E9B77512D37EC400DA6239 /* optionparser.cpp */,
+                               A7E9B77612D37EC400DA6239 /* optionparser.h */,
+                               A7E9B77B12D37EC400DA6239 /* overlap.cpp */,
+                               A7E9B77C12D37EC400DA6239 /* overlap.hpp */,
+                               A7E9B79B12D37EC400DA6239 /* progress.cpp */,
+                               A7E9B79C12D37EC400DA6239 /* progress.hpp */,
+                               A7E9B7A512D37EC400DA6239 /* rarecalc.cpp */,
+                               A7E9B7A612D37EC400DA6239 /* rarecalc.h */,
+                               A7E9B7A712D37EC400DA6239 /* raredisplay.cpp */,
+                               A7E9B7A812D37EC400DA6239 /* raredisplay.h */,
+                               A7E9B7A912D37EC400DA6239 /* rarefact.cpp */,
+                               A7E9B7AA12D37EC400DA6239 /* rarefact.h */,
+                               A7E9B7AD12D37EC400DA6239 /* rarefactioncurvedata.h */,
+                               A7E9BA5312D39A5E00DA6239 /* read */,
+                               A7E9B76112D37EC400DA6239 /* nast.cpp */,
+                               A7E9B76212D37EC400DA6239 /* nast.hpp */,
+                               A7E9B76312D37EC400DA6239 /* nastreport.cpp */,
+                               A7E9B76412D37EC400DA6239 /* nastreport.hpp */,
+                               A7E9B76712D37EC400DA6239 /* noalign.cpp */,
+                               A7E9B76812D37EC400DA6239 /* noalign.hpp */,
+                               A7E9B82312D37EC400DA6239 /* sharedutilities.cpp */,
+                               A7E9B82412D37EC400DA6239 /* sharedutilities.h */,
+                               A7E9B82D12D37EC400DA6239 /* singlelinkage.cpp */,
+                               A7E9B83012D37EC400DA6239 /* slibshuff.cpp */,
+                               A7E9B83112D37EC400DA6239 /* slibshuff.h */,
+                               A7E9B85112D37EC400DA6239 /* suffixdb.cpp */,
+                               A7E9B85212D37EC400DA6239 /* suffixdb.hpp */,
+                               A7E9B85312D37EC400DA6239 /* suffixnodes.cpp */,
+                               A7E9B85412D37EC400DA6239 /* suffixnodes.hpp */,
+                               A7E9B85512D37EC400DA6239 /* suffixtree.cpp */,
+                               A7E9B85612D37EC400DA6239 /* suffixtree.hpp */,
+                               A7E9B87412D37EC400DA6239 /* validcalculator.cpp */,
+                               A7E9B87512D37EC400DA6239 /* validcalculator.h */,
+                               A7E9B87612D37EC400DA6239 /* validparameter.cpp */,
+                               A7E9B87712D37EC400DA6239 /* validparameter.h */,
+                               A7E9B87812D37EC400DA6239 /* venn.cpp */,
+                               A7E9B87912D37EC400DA6239 /* venn.h */,
+                               A7E9B87E12D37EC400DA6239 /* weightedlinkage.cpp */,
                        );
-                       name = calculators;
+                       name = Source;
                        sourceTree = "<group>";
                };
-               A7CB593E11402F110010EB83 /* commands */ = {
+               1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               7E1CA7D912C2A425003F10B2 /* trimflowscommand.h */,
-                               7E1CA7DA12C2A425003F10B2 /* trimflowscommand.cpp */,
-                               A7DA202B113FECD400BF472F /* command.hpp */,
-                               A7DA1FEF113FECD400BF472F /* aligncommand.h */,
-                               A7DA1FEE113FECD400BF472F /* aligncommand.cpp */,
-                               A7DA1FFE113FECD400BF472F /* binsequencecommand.h */,
-                               A7DA1FFD113FECD400BF472F /* binsequencecommand.cpp */,
-                               A7DA2008113FECD400BF472F /* bootstrapsharedcommand.h */,
-                               A7DA2007113FECD400BF472F /* bootstrapsharedcommand.cpp */,
-                               A7D216061199C47F00F13F13 /* catchallcommand.h */,
-                               A7D216071199C47F00F13F13 /* catchallcommand.cpp */,
-                               A7DA2018113FECD400BF472F /* chimeraseqscommand.h */,
-                               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 */,
-                               A7DA201D113FECD400BF472F /* classifyseqscommand.cpp */,
-                               A7BBDA7B11B5694E006E6551 /* classifyotucommand.h */,
-                               A7BBDA7C11B5694E006E6551 /* classifyotucommand.cpp */,
-                               A7D215C811996C6E00F13F13 /* clearcutcommand.h */,
-                               A7D215C911996C6E00F13F13 /* clearcutcommand.cpp */,
-                               A7DA2022113FECD400BF472F /* clustercommand.h */,
-                               A7DA2021113FECD400BF472F /* clustercommand.cpp */,
-                               A7653D111278B09C009D6C09 /* clusterdoturcommand.h */,
-                               A7653D121278B09C009D6C09 /* clusterdoturcommand.cpp */,
-                               A74A9C03124B72DB000D5D25 /* clusterfragmentscommand.h */,
-                               A74A9C04124B72DB000D5D25 /* clusterfragmentscommand.cpp */,
-                               A71D924311AEB42400D00CBC /* clustersplitcommand.h */,
-                               A71D924211AEB42400D00CBC /* clustersplitcommand.cpp */,
-                               A7DA2026113FECD400BF472F /* collectcommand.h */,
-                               A7DA2025113FECD400BF472F /* collectcommand.cpp */,
-                               A7DA202A113FECD400BF472F /* collectsharedcommand.h */,
-                               A7DA2029113FECD400BF472F /* collectsharedcommand.cpp */,
-                               A7DA2032113FECD400BF472F /* consensuscommand.h */,
-                               A7DA2031113FECD400BF472F /* consensuscommand.cpp */,
-                               A71FF438129BDC35004397E6 /* consensusseqscommand.h */,
-                               A71FF439129BDC35004397E6 /* consensusseqscommand.cpp */,
-                               A7D9006D12C2544A00D8F543 /* corraxescommand.h */,
-                               A7D9006E12C2544A00D8F543 /* corraxescommand.cpp */,
-                               A7118EE511CFCAC000CFDE03 /* degapseqscommand.h */,
-                               A7118EE611CFCAC000CFDE03 /* degapseqscommand.cpp */,
-                               A7DA203B113FECD400BF472F /* deconvolutecommand.h */,
-                               A7DA203A113FECD400BF472F /* deconvolutecommand.cpp */,
-                               A7DA203F113FECD400BF472F /* distancecommand.h */,
-                               A7DA203E113FECD400BF472F /* distancecommand.cpp */,
-                               A76714DD126DE45A003F359A /* deuniqueseqscommand.h */,
-                               A76714DE126DE45A003F359A /* deuniqueseqscommand.cpp */,
-                               A7DA2050113FECD400BF472F /* filterseqscommand.h */,
-                               A7DA204F113FECD400BF472F /* filterseqscommand.cpp */,
-                               A7DA205B113FECD400BF472F /* getgroupcommand.h */,
-                               A7DA205A113FECD400BF472F /* getgroupcommand.cpp */,
-                               A75103D6128AE34100ABB831 /* getgroupscommand.h */,
-                               A75103D7128AE34100ABB831 /* getgroupscommand.cpp */,
-                               A7DA205D113FECD400BF472F /* getlabelcommand.h */,
-                               A7DA205C113FECD400BF472F /* getlabelcommand.cpp */,
-                               A787A24F124CB46C0076EB84 /* getlineagecommand.h */,
-                               A787A250124CB46C0076EB84 /* getlineagecommand.cpp */,
-                               A7DA205F113FECD400BF472F /* getlistcountcommand.h */,
-                               A7DA205E113FECD400BF472F /* getlistcountcommand.cpp */,
-                               A7510407128AFCC100ABB831 /* getotuscommand.h */,
-                               A7510408128AFCC100ABB831 /* getotuscommand.cpp */,
-                               A7DA2061113FECD400BF472F /* getoturepcommand.h */,
-                               A7DA2060113FECD400BF472F /* getoturepcommand.cpp */,
-                               A7DA2063113FECD400BF472F /* getrabundcommand.h */,
-                               A7DA2062113FECD400BF472F /* getrabundcommand.cpp */,
-                               A7118F0F11CFD5DC00CFDE03 /* getrelabundcommand.h */,
-                               A7118F1011CFD5DC00CFDE03 /* getrelabundcommand.cpp */,
-                               A7DA2065113FECD400BF472F /* getsabundcommand.h */,
-                               A7DA2064113FECD400BF472F /* getsabundcommand.cpp */,
-                               A7DA2067113FECD400BF472F /* getseqscommand.h */,
-                               A7DA2066113FECD400BF472F /* getseqscommand.cpp */,
-                               A7DA2069113FECD400BF472F /* getsharedotucommand.h */,
-                               A7DA2068113FECD400BF472F /* getsharedotucommand.cpp */,
-                               A7DA2075113FECD400BF472F /* hclustercommand.h */,
-                               A7DA2074113FECD400BF472F /* hclustercommand.cpp */,
-                               A7DA2079113FECD400BF472F /* heatmapcommand.h */,
-                               A7DA2078113FECD400BF472F /* heatmapcommand.cpp */,
-                               A7DA207D113FECD400BF472F /* heatmapsimcommand.h */,
-                               A7DA207C113FECD400BF472F /* heatmapsimcommand.cpp */,
-                               A7DA207F113FECD400BF472F /* helpcommand.h */,
-                               A7DA207E113FECD400BF472F /* helpcommand.cpp */,
-                               A76D1473128D9DA2005D4DFE /* indicatorcommand.h */,
-                               A76D1474128D9DA2005D4DFE /* indicatorcommand.cpp */,
-                               A7DA208E113FECD400BF472F /* libshuffcommand.h */,
-                               A7DA208D113FECD400BF472F /* libshuffcommand.cpp */,
-                               A7DA2090113FECD400BF472F /* listseqscommand.h */,
-                               A7DA208F113FECD400BF472F /* listseqscommand.cpp */,
-                               A703FE931194645F002C397E /* makegroupcommand.h */,
-                               A703FE941194645F002C397E /* makegroupcommand.cpp */,
-                               A7DA2099113FECD400BF472F /* matrixoutputcommand.h */,
-                               A7DA2098113FECD400BF472F /* matrixoutputcommand.cpp */,
-                               A7DA209B113FECD400BF472F /* mergefilecommand.h */,
-                               A7DA209A113FECD400BF472F /* mergefilecommand.cpp */,
-                               A7F6C8EA12423C0300299875 /* metastatscommand.h */,
-                               A7F6C8EB12423C0300299875 /* metastatscommand.cpp */,
-                               A7DA209D113FECD400BF472F /* mgclustercommand.h */,
-                               A7DA209C113FECD400BF472F /* mgclustercommand.cpp */,
-                               A7DA20AD113FECD400BF472F /* nocommands.h */,
-                               A7DA20AC113FECD400BF472F /* nocommands.cpp */,
-                               A798626D1240D91B005FC847 /* normalizesharedcommand.h */,
-                               A798626E1240D91B005FC847 /* normalizesharedcommand.cpp */,
-                               A7DA20B9113FECD400BF472F /* otuhierarchycommand.h */,
-                               A7DA20B8113FECD400BF472F /* otuhierarchycommand.cpp */,
-                               A77D787B126F387700F351BD /* pairwiseseqscommand.h */,
-                               A77D787C126F387700F351BD /* pairwiseseqscommand.cpp */,
-                               A724C2B61254961E006BB1C7 /* parsefastaqcommand.h */,
-                               A724C2B71254961E006BB1C7 /* parsefastaqcommand.cpp */,
-                               A7DA20BD113FECD400BF472F /* parselistscommand.h */,
-                               A7DA20BC113FECD400BF472F /* parselistscommand.cpp */,
-                               A7DA20C1113FECD400BF472F /* parsimonycommand.h */,
-                               A7DA20C0113FECD400BF472F /* parsimonycommand.cpp */,
-                               A7DA20C3113FECD400BF472F /* pcacommand.h */,
-                               A7DA20C2113FECD400BF472F /* pcacommand.cpp */,
-                               A72B3A62118B37FD004B9F8D /* phylodiversitycommand.h */,
-                               A72B3A63118B37FD004B9F8D /* phylodiversitycommand.cpp */,
-                               A7DA20C7113FECD400BF472F /* phylotypecommand.h */,
-                               A7DA20C6113FECD400BF472F /* phylotypecommand.cpp */,
-                               A72C66A1125B356F0058C2F9 /* pipelinepdscommand.h */,
-                               A72C66A2125B356F0058C2F9 /* pipelinepdscommand.cpp */,
-                               A7DA20CB113FECD400BF472F /* preclustercommand.h */,
-                               A7DA20CA113FECD400BF472F /* preclustercommand.cpp */,
-                               A7DA20D1113FECD400BF472F /* quitcommand.h */,
-                               A7DA20D0113FECD400BF472F /* quitcommand.cpp */,
-                               A7DA20DB113FECD400BF472F /* rarefactcommand.h */,
-                               A7DA20DA113FECD400BF472F /* rarefactcommand.cpp */,
-                               A7DA20DE113FECD400BF472F /* rarefactsharedcommand.h */,
-                               A7DA20DD113FECD400BF472F /* rarefactsharedcommand.cpp */,
-                               A7DA20E6113FECD400BF472F /* readdistcommand.h */,
-                               A7DA20E5113FECD400BF472F /* readdistcommand.cpp */,
-                               A7DA20EB113FECD400BF472F /* readotucommand.h */,
-                               A7DA20EA113FECD400BF472F /* readotucommand.cpp */,
-                               A7DA20F1113FECD400BF472F /* readtreecommand.h */,
-                               A7DA20F0113FECD400BF472F /* readtreecommand.cpp */,
-                               A751032A128AC93F00ABB831 /* removegroupscommand.h */,
-                               A751032B128AC93F00ABB831 /* removegroupscommand.cpp */,
-                               A787A28E124CE1470076EB84 /* removelineagecommand.h */,
-                               A787A28F124CE1470076EB84 /* removelineagecommand.cpp */,
-                               A76D1451128D6A03005D4DFE /* removeotuscommand.h */,
-                               A76D1452128D6A03005D4DFE /* removeotuscommand.cpp */,
-                               A7DA20F3113FECD400BF472F /* removeseqscommand.h */,
-                               A7DA20F2113FECD400BF472F /* removeseqscommand.cpp */,
-                               A7DA20F5113FECD400BF472F /* reversecommand.h */,
-                               A7DA20F4113FECD400BF472F /* reversecommand.cpp */,
-                               A7DA20F9113FECD400BF472F /* screenseqscommand.h */,
-                               A7DA20F8113FECD400BF472F /* screenseqscommand.cpp */,
-                               A7DA20FB113FECD400BF472F /* secondarystructurecommand.h */,
-                               A7DA20FA113FECD400BF472F /* secondarystructurecommand.cpp */,
-                               7EA299BA11E384940022D8D3 /* sensspeccommand.h */,
-                               7EA299BB11E384940022D8D3 /* sensspeccommand.cpp */,
-                               7E84528511EF4BEB00564975 /* seqerrorcommand.h */,
-                               7E84528611EF4BEB00564975 /* seqerrorcommand.cpp */,
-                               A7DA20FD113FECD400BF472F /* seqsummarycommand.h */,
-                               A7DA20FC113FECD400BF472F /* seqsummarycommand.cpp */,
-                               A7DA2103113FECD400BF472F /* setdircommand.h */,
-                               A7DA2102113FECD400BF472F /* setdircommand.cpp */,
-                               A76C4A1011876BAF0009460B /* setlogfilecommand.h */,
-                               A76C4A1111876BAF0009460B /* setlogfilecommand.cpp */,
-                               A732505E11E49EF100484B90 /* sffinfocommand.h */,
-                               A732505F11E49EF100484B90 /* sffinfocommand.cpp */,
-                               A7DA2110113FECD400BF472F /* sharedcommand.h */,
-                               A7DA210F113FECD400BF472F /* sharedcommand.cpp */,
-                               A71D924511AEB42400D00CBC /* splitabundcommand.h */,
-                               A71D924411AEB42400D00CBC /* splitabundcommand.cpp */,
-                               A7F139481247C3CB0033324C /* splitgroupscommand.h */,
-                               A7F139491247C3CB0033324C /* splitgroupscommand.cpp */,
-                               A7653CB112789EFD009D6C09 /* subsamplecommand.h */,
-                               A7653CB212789EFD009D6C09 /* subsamplecommand.cpp */,
-                               A7DA2155113FECD400BF472F /* summarycommand.h */,
-                               A7DA2154113FECD400BF472F /* summarycommand.cpp */,
-                               A7DA2159113FECD400BF472F /* summarysharedcommand.h */,
-                               A7DA2158113FECD400BF472F /* summarysharedcommand.cpp */,
-                               A7DA215B113FECD400BF472F /* systemcommand.h */,
-                               A7DA215A113FECD400BF472F /* systemcommand.cpp */,
-                               A7DA2162113FECD400BF472F /* treegroupscommand.h */,
-                               A7DA2161113FECD400BF472F /* treegroupscommand.cpp */,
-                               A7DA2168113FECD400BF472F /* trimseqscommand.h */,
-                               A7DA2167113FECD400BF472F /* trimseqscommand.cpp */,
-                               A7DA216A113FECD400BF472F /* unifracunweightedcommand.h */,
-                               A7DA2169113FECD400BF472F /* unifracunweightedcommand.cpp */,
-                               A7DA216C113FECD400BF472F /* unifracweightedcommand.h */,
-                               A7DA216B113FECD400BF472F /* unifracweightedcommand.cpp */,
-                               A7DA2178113FECD400BF472F /* venncommand.h */,
-                               A7DA2177113FECD400BF472F /* venncommand.cpp */,
+                               8DD76FB20486AB0100D96B5E /* mothur */,
+                       );
+                       name = Products;
+                       sourceTree = "<group>";
+               };
+               A7E9BA3812D3956100DA6239 /* commands */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7E9B6AE12D37EC400DA6239 /* command.hpp */,
+                               A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
+                               A7E9B65212D37EC300DA6239 /* aligncommand.h */,
+                               A7E9B66012D37EC300DA6239 /* binsequencecommand.cpp */,
+                               A7E9B66112D37EC300DA6239 /* binsequencecommand.h */,
+                               A7E9B66A12D37EC400DA6239 /* bootstrapsharedcommand.cpp */,
+                               A7E9B66B12D37EC400DA6239 /* bootstrapsharedcommand.h */,
+                               A7E9B67212D37EC400DA6239 /* catchallcommand.cpp */,
+                               A7E9B67312D37EC400DA6239 /* catchallcommand.h */,
+                               A7E9B67A12D37EC400DA6239 /* chimerabellerophoncommand.cpp */,
+                               A7E9B67B12D37EC400DA6239 /* chimerabellerophoncommand.h */,
+                               A7E9B67C12D37EC400DA6239 /* chimeraccodecommand.cpp */,
+                               A7E9B67D12D37EC400DA6239 /* chimeraccodecommand.h */,
+                               A7E9B67E12D37EC400DA6239 /* chimeracheckcommand.cpp */,
+                               A7E9B67F12D37EC400DA6239 /* chimeracheckcommand.h */,
+                               A7E9B68212D37EC400DA6239 /* chimerapintailcommand.cpp */,
+                               A7E9B68312D37EC400DA6239 /* chimerapintailcommand.h */,
+                               A7E9B68612D37EC400DA6239 /* chimeraseqscommand.cpp */,
+                               A7E9B68712D37EC400DA6239 /* chimeraseqscommand.h */,
+                               A7E9B68A12D37EC400DA6239 /* chimeraslayercommand.cpp */,
+                               A7E9B68B12D37EC400DA6239 /* chimeraslayercommand.h */,
+                               A7E9B68C12D37EC400DA6239 /* chopseqscommand.cpp */,
+                               A7E9B68D12D37EC400DA6239 /* chopseqscommand.h */,
+                               A7E9B69012D37EC400DA6239 /* classifyotucommand.cpp */,
+                               A7E9B69112D37EC400DA6239 /* classifyotucommand.h */,
+                               A7E9B69212D37EC400DA6239 /* classifyseqscommand.cpp */,
+                               A7E9B69312D37EC400DA6239 /* classifyseqscommand.h */,
+                               A7E9B69612D37EC400DA6239 /* clearcutcommand.cpp */,
+                               A7E9B69712D37EC400DA6239 /* clearcutcommand.h */,
+                               A7E9B69C12D37EC400DA6239 /* clustercommand.cpp */,
+                               A7E9B69D12D37EC400DA6239 /* clustercommand.h */,
+                               A7E9B69E12D37EC400DA6239 /* clusterdoturcommand.cpp */,
+                               A7E9B69F12D37EC400DA6239 /* clusterdoturcommand.h */,
+                               A7E9B6A012D37EC400DA6239 /* clusterfragmentscommand.cpp */,
+                               A7E9B6A112D37EC400DA6239 /* clusterfragmentscommand.h */,
+                               A7E9B6A212D37EC400DA6239 /* clustersplitcommand.cpp */,
+                               A7E9B6A312D37EC400DA6239 /* clustersplitcommand.h */,
+                               A7E9B6A812D37EC400DA6239 /* collectcommand.cpp */,
+                               A7E9B6A912D37EC400DA6239 /* collectcommand.h */,
+                               A7E9B6AC12D37EC400DA6239 /* collectsharedcommand.cpp */,
+                               A7E9B6AD12D37EC400DA6239 /* collectsharedcommand.h */,
+                               A7E9B6B512D37EC400DA6239 /* consensuscommand.cpp */,
+                               A7E9B6B612D37EC400DA6239 /* consensuscommand.h */,
+                               A7E9B6B712D37EC400DA6239 /* consensusseqscommand.cpp */,
+                               A7E9B6B812D37EC400DA6239 /* consensusseqscommand.h */,
+                               A7E9B6B912D37EC400DA6239 /* corraxescommand.cpp */,
+                               A7E9B6BA12D37EC400DA6239 /* corraxescommand.h */,
+                               A7E9B6C312D37EC400DA6239 /* deconvolutecommand.cpp */,
+                               A7E9B6C412D37EC400DA6239 /* deconvolutecommand.h */,
+                               A7E9B6C512D37EC400DA6239 /* degapseqscommand.cpp */,
+                               A7E9B6C612D37EC400DA6239 /* degapseqscommand.h */,
+                               A7E9B6C712D37EC400DA6239 /* deuniqueseqscommand.cpp */,
+                               A7E9B6C812D37EC400DA6239 /* deuniqueseqscommand.h */,
+                               A7E9B6CB12D37EC400DA6239 /* distancecommand.cpp */,
+                               A7E9B6CC12D37EC400DA6239 /* distancecommand.h */,
+                               A7E9B6E312D37EC400DA6239 /* filterseqscommand.cpp */,
+                               A7E9B6E412D37EC400DA6239 /* filterseqscommand.h */,
+                               A7E9B6F212D37EC400DA6239 /* getgroupcommand.cpp */,
+                               A7E9B6F312D37EC400DA6239 /* getgroupcommand.h */,
+                               A7E9B6F412D37EC400DA6239 /* getgroupscommand.cpp */,
+                               A7E9B6F512D37EC400DA6239 /* getgroupscommand.h */,
+                               A7E9B6F612D37EC400DA6239 /* getlabelcommand.cpp */,
+                               A7E9B6F712D37EC400DA6239 /* getlabelcommand.h */,
+                               A7E9B6F812D37EC400DA6239 /* getlineagecommand.cpp */,
+                               A7E9B6F912D37EC400DA6239 /* getlineagecommand.h */,
+                               A7E9B6FA12D37EC400DA6239 /* getlistcountcommand.cpp */,
+                               A7E9B6FB12D37EC400DA6239 /* getlistcountcommand.h */,
+                               A7E9B6FE12D37EC400DA6239 /* getoturepcommand.cpp */,
+                               A7E9B6FF12D37EC400DA6239 /* getoturepcommand.h */,
+                               A7E9B70012D37EC400DA6239 /* getotuscommand.cpp */,
+                               A7E9B70112D37EC400DA6239 /* getotuscommand.h */,
+                               A7E9B70212D37EC400DA6239 /* getrabundcommand.cpp */,
+                               A7E9B70312D37EC400DA6239 /* getrabundcommand.h */,
+                               A7E9B70412D37EC400DA6239 /* getrelabundcommand.cpp */,
+                               A7E9B70512D37EC400DA6239 /* getrelabundcommand.h */,
+                               A7E9B70612D37EC400DA6239 /* getsabundcommand.cpp */,
+                               A7E9B70712D37EC400DA6239 /* getsabundcommand.h */,
+                               A7E9B70812D37EC400DA6239 /* getseqscommand.cpp */,
+                               A7E9B70912D37EC400DA6239 /* getseqscommand.h */,
+                               A7E9B70A12D37EC400DA6239 /* getsharedotucommand.cpp */,
+                               A7E9B70B12D37EC400DA6239 /* getsharedotucommand.h */,
+                               A7E9B71A12D37EC400DA6239 /* hclustercommand.cpp */,
+                               A7E9B71B12D37EC400DA6239 /* hclustercommand.h */,
+                               A7E9B71E12D37EC400DA6239 /* heatmapcommand.cpp */,
+                               A7E9B71F12D37EC400DA6239 /* heatmapcommand.h */,
+                               A7E9B72212D37EC400DA6239 /* heatmapsimcommand.cpp */,
+                               A7E9B72312D37EC400DA6239 /* heatmapsimcommand.h */,
+                               A7E9B72812D37EC400DA6239 /* helpcommand.cpp */,
+                               A7E9B72912D37EC400DA6239 /* helpcommand.h */,
+                               A7E9B72B12D37EC400DA6239 /* indicatorcommand.cpp */,
+                               A7E9B72C12D37EC400DA6239 /* indicatorcommand.h */,
+                               A7E9B73B12D37EC400DA6239 /* libshuffcommand.cpp */,
+                               A7E9B73C12D37EC400DA6239 /* libshuffcommand.h */,
+                               A7E9B73D12D37EC400DA6239 /* listseqscommand.cpp */,
+                               A7E9B73E12D37EC400DA6239 /* listseqscommand.h */,
+                               A7E9B74312D37EC400DA6239 /* makegroupcommand.cpp */,
+                               A7E9B74412D37EC400DA6239 /* makegroupcommand.h */,
+                               A7E9B74912D37EC400DA6239 /* matrixoutputcommand.cpp */,
+                               A7E9B74A12D37EC400DA6239 /* matrixoutputcommand.h */,
+                               A7E9B75312D37EC400DA6239 /* mergefilecommand.cpp */,
+                               A7E9B75412D37EC400DA6239 /* mergefilecommand.h */,
+                               A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
+                               A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
+                               A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
+                               A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */,
+                               A7E9B76A12D37EC400DA6239 /* nocommands.h */,
+                               A7E9B76912D37EC400DA6239 /* nocommands.cpp */,
+                               A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
+                               A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */,
+                               A7E9B77912D37EC400DA6239 /* otuhierarchycommand.cpp */,
+                               A7E9B77A12D37EC400DA6239 /* otuhierarchycommand.h */,
+                               A7E9B77D12D37EC400DA6239 /* pairwiseseqscommand.cpp */,
+                               A7E9B77E12D37EC400DA6239 /* pairwiseseqscommand.h */,
+                               A7E9B77F12D37EC400DA6239 /* parsefastaqcommand.cpp */,
+                               A7E9B78012D37EC400DA6239 /* parsefastaqcommand.h */,
+                               A7E9B78112D37EC400DA6239 /* parselistscommand.cpp */,
+                               A7E9B78212D37EC400DA6239 /* parselistscommand.h */,
+                               A7E9B78512D37EC400DA6239 /* parsimonycommand.cpp */,
+                               A7E9B78612D37EC400DA6239 /* parsimonycommand.h */,
+                               A7E9B78712D37EC400DA6239 /* pcacommand.cpp */,
+                               A7E9B78812D37EC400DA6239 /* pcacommand.h */,
+                               A7E9B78B12D37EC400DA6239 /* phylodiversitycommand.cpp */,
+                               A7E9B78C12D37EC400DA6239 /* phylodiversitycommand.h */,
+                               A7E9B79112D37EC400DA6239 /* phylotypecommand.cpp */,
+                               A7E9B79212D37EC400DA6239 /* phylotypecommand.h */,
+                               A7E9B79512D37EC400DA6239 /* pipelinepdscommand.cpp */,
+                               A7E9B79612D37EC400DA6239 /* pipelinepdscommand.h */,
+                               A7E9B79712D37EC400DA6239 /* preclustercommand.cpp */,
+                               A7E9B79812D37EC400DA6239 /* preclustercommand.h */,
+                               A7E9B7A112D37EC400DA6239 /* quitcommand.cpp */,
+                               A7E9B7A212D37EC400DA6239 /* quitcommand.h */,
+                               A7E9B7AB12D37EC400DA6239 /* rarefactcommand.cpp */,
+                               A7E9B7AC12D37EC400DA6239 /* rarefactcommand.h */,
+                               A7E9B7AE12D37EC400DA6239 /* rarefactsharedcommand.cpp */,
+                               A7E9B7AF12D37EC400DA6239 /* rarefactsharedcommand.h */,
+                               A7E9B7B612D37EC400DA6239 /* readdistcommand.cpp */,
+                               A7E9B7B712D37EC400DA6239 /* readdistcommand.h */,
+                               A7E9B7BB12D37EC400DA6239 /* readotucommand.cpp */,
+                               A7E9B7BC12D37EC400DA6239 /* readotucommand.h */,
+                               A7E9B7C112D37EC400DA6239 /* readtreecommand.cpp */,
+                               A7E9B7C212D37EC400DA6239 /* readtreecommand.h */,
+                               A7E9B7C312D37EC400DA6239 /* removegroupscommand.cpp */,
+                               A7E9B7C412D37EC400DA6239 /* removegroupscommand.h */,
+                               A7E9B7C512D37EC400DA6239 /* removelineagecommand.cpp */,
+                               A7E9B7C612D37EC400DA6239 /* removelineagecommand.h */,
+                               A7E9B7C712D37EC400DA6239 /* removeotuscommand.cpp */,
+                               A7E9B7C812D37EC400DA6239 /* removeotuscommand.h */,
+                               A7E9B7C912D37EC400DA6239 /* removeseqscommand.cpp */,
+                               A7E9B7CA12D37EC400DA6239 /* removeseqscommand.h */,
+                               A7E9B7CD12D37EC400DA6239 /* reversecommand.cpp */,
+                               A7E9B7CE12D37EC400DA6239 /* reversecommand.h */,
+                               A7E9B7D112D37EC400DA6239 /* screenseqscommand.cpp */,
+                               A7E9B7D212D37EC400DA6239 /* screenseqscommand.h */,
+                               A7E9B7D312D37EC400DA6239 /* secondarystructurecommand.cpp */,
+                               A7E9B7D412D37EC400DA6239 /* secondarystructurecommand.h */,
+                               A7E9B7D512D37EC400DA6239 /* sensspeccommand.cpp */,
+                               A7E9B7D612D37EC400DA6239 /* sensspeccommand.h */,
+                               A7E9B7D712D37EC400DA6239 /* seqerrorcommand.cpp */,
+                               A7E9B7D812D37EC400DA6239 /* seqerrorcommand.h */,
+                               A7E9B7D912D37EC400DA6239 /* seqsummarycommand.cpp */,
+                               A7E9B7DA12D37EC400DA6239 /* seqsummarycommand.h */,
+                               A7E9B7DF12D37EC400DA6239 /* setdircommand.cpp */,
+                               A7E9B7E012D37EC400DA6239 /* setdircommand.h */,
+                               A7E9B7E112D37EC400DA6239 /* setlogfilecommand.cpp */,
+                               A7E9B7E212D37EC400DA6239 /* setlogfilecommand.h */,
+                               A7E9B7E312D37EC400DA6239 /* sffinfocommand.cpp */,
+                               A7E9B7E412D37EC400DA6239 /* sffinfocommand.h */,
+                               A7E9B7F212D37EC400DA6239 /* sharedcommand.cpp */,
+                               A7E9B7F312D37EC400DA6239 /* sharedcommand.h */,
+                               A7E9B82712D37EC400DA6239 /* shhhercommand.cpp */,
+                               A7E9B82812D37EC400DA6239 /* shhhercommand.h */,
+                               A7E9B83F12D37EC400DA6239 /* splitabundcommand.cpp */,
+                               A7E9B84012D37EC400DA6239 /* splitabundcommand.h */,
+                               A7E9B84112D37EC400DA6239 /* splitgroupscommand.cpp */,
+                               A7E9B84212D37EC400DA6239 /* splitgroupscommand.h */,
+                               A7E9B84F12D37EC400DA6239 /* subsamplecommand.cpp */,
+                               A7E9B85012D37EC400DA6239 /* subsamplecommand.h */,
+                               A7E9B85712D37EC400DA6239 /* summarycommand.cpp */,
+                               A7E9B85812D37EC400DA6239 /* summarycommand.h */,
+                               A7E9B85912D37EC400DA6239 /* summarysharedcommand.cpp */,
+                               A7E9B85A12D37EC400DA6239 /* summarysharedcommand.h */,
+                               A7E9B85B12D37EC400DA6239 /* systemcommand.cpp */,
+                               A7E9B85C12D37EC400DA6239 /* systemcommand.h */,
+                               A7E9B86212D37EC400DA6239 /* treegroupscommand.cpp */,
+                               A7E9B86312D37EC400DA6239 /* treegroupscommand.h */,
+                               A7E9B86812D37EC400DA6239 /* trimflowscommand.cpp */,
+                               A7E9B86912D37EC400DA6239 /* trimflowscommand.h */,
+                               A7E9B86A12D37EC400DA6239 /* trimseqscommand.cpp */,
+                               A7E9B86B12D37EC400DA6239 /* trimseqscommand.h */,
+                               A7E9B86C12D37EC400DA6239 /* unifracunweightedcommand.cpp */,
+                               A7E9B86D12D37EC400DA6239 /* unifracunweightedcommand.h */,
+                               A7E9B86E12D37EC400DA6239 /* unifracweightedcommand.cpp */,
+                               A7E9B86F12D37EC400DA6239 /* unifracweightedcommand.h */,
+                               A7E9B87A12D37EC400DA6239 /* venncommand.cpp */,
+                               A7E9B87B12D37EC400DA6239 /* venncommand.h */,
                        );
                        name = commands;
                        sourceTree = "<group>";
                };
-               A7CB594211402F430010EB83 /* containers */ = {
+               A7E9BA3F12D395F700DA6239 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
-                               A7DA1FF3113FECD400BF472F /* alignmentcell.hpp */,
-                               A7DA1FF2113FECD400BF472F /* alignmentcell.cpp */,
-                               A7DA1FF4113FECD400BF472F /* alignmentdb.cpp */,
-                               A7DA1FF5113FECD400BF472F /* alignmentdb.h */,
-                               A7DA2001113FECD400BF472F /* blastdb.cpp */,
-                               A7DA2002113FECD400BF472F /* blastdb.hpp */,
-                               A7DA2035113FECD400BF472F /* database.cpp */,
-                               A7DA2036113FECD400BF472F /* database.hpp */,
-                               A7DA2037113FECD400BF472F /* datavector.hpp */,
-                               A7DA2040113FECD400BF472F /* distancedb.cpp */,
-                               A7DA2041113FECD400BF472F /* distancedb.hpp */,
-                               A7DA204A113FECD400BF472F /* fastamap.cpp */,
-                               A7DA204B113FECD400BF472F /* fastamap.h */,
-                               A7DA2056113FECD400BF472F /* fullmatrix.cpp */,
-                               A7DA2057113FECD400BF472F /* fullmatrix.h */,
-                               A7DA2070113FECD400BF472F /* groupmap.cpp */,
-                               A7DA2071113FECD400BF472F /* groupmap.h */,
-                               A7DA2085113FECD400BF472F /* kmer.cpp */,
-                               A7DA2086113FECD400BF472F /* kmer.hpp */,
-                               A7DA2087113FECD400BF472F /* kmerdb.cpp */,
-                               A7DA2088113FECD400BF472F /* kmerdb.hpp */,
-                               A7DA2091113FECD400BF472F /* listvector.cpp */,
-                               A7DA2092113FECD400BF472F /* listvector.hpp */,
-                               A7DA20A2113FECD400BF472F /* nameassignment.cpp */,
-                               A7DA20A3113FECD400BF472F /* nameassignment.hpp */,
-                               A7DA20B6113FECD400BF472F /* ordervector.cpp */,
-                               A7DA20B7113FECD400BF472F /* ordervector.hpp */,
-                               7E85BD1C11EB5E9B00FD37C0 /* qualityscores.h */,
-                               7E85BD1D11EB5E9B00FD37C0 /* qualityscores.cpp */,
-                               A7DA20D3113FECD400BF472F /* rabundvector.hpp */,
-                               A7DA20D2113FECD400BF472F /* rabundvector.cpp */,
-                               A7DA20F6113FECD400BF472F /* sabundvector.cpp */,
-                               A7DA20F7113FECD400BF472F /* sabundvector.hpp */,
-                               A7DA20FE113FECD400BF472F /* sequence.cpp */,
-                               A7DA20FF113FECD400BF472F /* sequence.hpp */,
-                               A7DA2100113FECD400BF472F /* sequencedb.cpp */,
-                               A7DA2101113FECD400BF472F /* sequencedb.h */,
-                               A7DA2121113FECD400BF472F /* sharedlistvector.cpp */,
-                               A7DA2122113FECD400BF472F /* sharedlistvector.h */,
-                               A7DA212A113FECD400BF472F /* sharedordervector.cpp */,
-                               A7DA212B113FECD400BF472F /* sharedordervector.h */,
-                               A7DA212C113FECD400BF472F /* sharedrabundvector.cpp */,
-                               A7DA212D113FECD400BF472F /* sharedrabundvector.h */,
-                               A7AE6302121C3408001DE6FC /* sharedrabundfloatvector.h */,
-                               A7AE6303121C3408001DE6FC /* sharedrabundfloatvector.cpp */,
-                               A7DA212F113FECD400BF472F /* sharedsabundvector.h */,
-                               A7DA212E113FECD400BF472F /* sharedsabundvector.cpp */,
-                               A7DA214C113FECD400BF472F /* sparsematrix.cpp */,
-                               A7DA214D113FECD400BF472F /* sparsematrix.hpp */,
-                               A7DA214E113FECD400BF472F /* suffixdb.cpp */,
-                               A7DA214F113FECD400BF472F /* suffixdb.hpp */,
-                               A7DA2150113FECD400BF472F /* suffixnodes.cpp */,
-                               A7DA2151113FECD400BF472F /* suffixnodes.hpp */,
-                               A7DA2152113FECD400BF472F /* suffixtree.cpp */,
-                               A7DA2153113FECD400BF472F /* suffixtree.hpp */,
-                               A7DA215E113FECD400BF472F /* tree.cpp */,
-                               A7DA215F113FECD400BF472F /* tree.h */,
-                               A7DA2163113FECD400BF472F /* treemap.cpp */,
-                               A7DA2164113FECD400BF472F /* treemap.h */,
-                               A7DA2165113FECD400BF472F /* treenode.cpp */,
-                               A7DA2166113FECD400BF472F /* treenode.h */,
+                               A7E9B64F12D37EC300DA6239 /* ace.cpp */,
+                               A7E9B65012D37EC300DA6239 /* ace.h */,
+                               A7E9B65E12D37EC300DA6239 /* bergerparker.cpp */,
+                               A7E9B65F12D37EC300DA6239 /* bergerparker.h */,
+                               A7E9B66612D37EC400DA6239 /* boneh.cpp */,
+                               A7E9B66712D37EC400DA6239 /* boneh.h */,
+                               A7E9B66812D37EC400DA6239 /* bootstrap.cpp */,
+                               A7E9B66912D37EC400DA6239 /* bootstrap.h */,
+                               A7E9B66C12D37EC400DA6239 /* bstick.cpp */,
+                               A7E9B66D12D37EC400DA6239 /* bstick.h */,
+                               A7E9B66E12D37EC400DA6239 /* calculator.cpp */,
+                               A7E9B66F12D37EC400DA6239 /* calculator.h */,
+                               A7E9B67012D37EC400DA6239 /* canberra.cpp */,
+                               A7E9B67112D37EC400DA6239 /* canberra.h */,
+                               A7E9B67612D37EC400DA6239 /* chao1.cpp */,
+                               A7E9B67712D37EC400DA6239 /* chao1.h */,
+                               A7E9B6A412D37EC400DA6239 /* cmdargs.cpp */,
+                               A7E9B6A512D37EC400DA6239 /* cmdargs.h */,
+                               A7E9B6BB12D37EC400DA6239 /* coverage.cpp */,
+                               A7E9B6BC12D37EC400DA6239 /* coverage.h */,
+                               A7E9B6CA12D37EC400DA6239 /* dist.h */,
+                               A7E9B6C012D37EC400DA6239 /* dayhoff.h */,
+                               A7E9B6D512D37EC400DA6239 /* eachgapdist.h */,
+                               A7E9B6D612D37EC400DA6239 /* eachgapignore.h */,
+                               A7E9B6D712D37EC400DA6239 /* efron.cpp */,
+                               A7E9B6D812D37EC400DA6239 /* efron.h */,
+                               A7E9B6E212D37EC400DA6239 /* filters.h */,
+                               A7E9B6E512D37EC400DA6239 /* fisher2.c */,
+                               A7E9B6E612D37EC400DA6239 /* fisher2.h */,
+                               A7E9B6F012D37EC400DA6239 /* geom.cpp */,
+                               A7E9B6F112D37EC400DA6239 /* geom.h */,
+                               A7E9B70E12D37EC400DA6239 /* goodscoverage.cpp */,
+                               A7E9B70F12D37EC400DA6239 /* goodscoverage.h */,
+                               A7E9B71212D37EC400DA6239 /* gower.cpp */,
+                               A7E9B71312D37EC400DA6239 /* gower.h */,
+                               A7E9B71612D37EC400DA6239 /* hamming.cpp */,
+                               A7E9B71712D37EC400DA6239 /* hamming.h */,
+                               A7E9B72412D37EC400DA6239 /* heip.cpp */,
+                               A7E9B72512D37EC400DA6239 /* heip.h */,
+                               A7E9B72612D37EC400DA6239 /* hellinger.cpp */,
+                               A7E9B72712D37EC400DA6239 /* hellinger.h */,
+                               A7E9B72A12D37EC400DA6239 /* ignoregaps.h */,
+                               A7E9B72F12D37EC400DA6239 /* invsimpson.cpp */,
+                               A7E9B73012D37EC400DA6239 /* invsimpson.h */,
+                               A7E9B73112D37EC400DA6239 /* jackknife.cpp */,
+                               A7E9B73212D37EC400DA6239 /* jackknife.h */,
+                               A7E9B74112D37EC400DA6239 /* logsd.cpp */,
+                               A7E9B74212D37EC400DA6239 /* logsd.h */,
+                               A7E9B74712D37EC400DA6239 /* manhattan.cpp */,
+                               A7E9B74812D37EC400DA6239 /* manhattan.h */,
+                               A7E9B74B12D37EC400DA6239 /* memchi2.cpp */,
+                               A7E9B74C12D37EC400DA6239 /* memchi2.h */,
+                               A7E9B74D12D37EC400DA6239 /* memchord.cpp */,
+                               A7E9B74E12D37EC400DA6239 /* memchord.h */,
+                               A7E9B74F12D37EC400DA6239 /* memeuclidean.cpp */,
+                               A7E9B75012D37EC400DA6239 /* memeuclidean.h */,
+                               A7E9B75112D37EC400DA6239 /* mempearson.cpp */,
+                               A7E9B75212D37EC400DA6239 /* mempearson.h */,
+                               A7E9B76D12D37EC400DA6239 /* npshannon.cpp */,
+                               A7E9B76E12D37EC400DA6239 /* npshannon.h */,
+                               A7E9B76F12D37EC400DA6239 /* nseqs.h */,
+                               A7E9B77112D37EC400DA6239 /* odum.cpp */,
+                               A7E9B77212D37EC400DA6239 /* odum.h */,
+                               A7E9B77312D37EC400DA6239 /* onegapdist.h */,
+                               A7E9B77412D37EC400DA6239 /* onegapignore.h */,
+                               A7E9B78412D37EC400DA6239 /* parsimony.h */,
+                               A7E9B78312D37EC400DA6239 /* parsimony.cpp */,
+                               A7E9B79912D37EC400DA6239 /* prng.cpp */,
+                               A7E9B79A12D37EC400DA6239 /* prng.h */,
+                               A7E9B79D12D37EC400DA6239 /* qstat.cpp */,
+                               A7E9B79E12D37EC400DA6239 /* qstat.h */,
+                               A7E9B7E512D37EC400DA6239 /* shannon.cpp */,
+                               A7E9B7E612D37EC400DA6239 /* shannon.h */,
+                               A7E9B7E712D37EC400DA6239 /* shannoneven.cpp */,
+                               A7E9B7E812D37EC400DA6239 /* shannoneven.h */,
+                               A7E9B7E912D37EC400DA6239 /* sharedace.cpp */,
+                               A7E9B7EA12D37EC400DA6239 /* sharedace.h */,
+                               A7E9B7EB12D37EC400DA6239 /* sharedanderberg.h */,
+                               A7E9B7EC12D37EC400DA6239 /* sharedanderbergs.cpp */,
+                               A7E9B7ED12D37EC400DA6239 /* sharedanderbergs.h */,
+                               A7E9B7EE12D37EC400DA6239 /* sharedbraycurtis.cpp */,
+                               A7E9B7EF12D37EC400DA6239 /* sharedbraycurtis.h */,
+                               A7E9B7F012D37EC400DA6239 /* sharedchao1.cpp */,
+                               A7E9B7F112D37EC400DA6239 /* sharedchao1.h */,
+                               A7E9B7F412D37EC400DA6239 /* sharedjabund.cpp */,
+                               A7E9B7F512D37EC400DA6239 /* sharedjabund.h */,
+                               A7E9B7F612D37EC400DA6239 /* sharedjackknife.cpp */,
+                               A7E9B7F712D37EC400DA6239 /* sharedjackknife.h */,
+                               A7E9B7F812D37EC400DA6239 /* sharedjclass.cpp */,
+                               A7E9B7F912D37EC400DA6239 /* sharedjclass.h */,
+                               A7E9B7FA12D37EC400DA6239 /* sharedjest.cpp */,
+                               A7E9B7FB12D37EC400DA6239 /* sharedjest.h */,
+                               A7E9B7FC12D37EC400DA6239 /* sharedkstest.cpp */,
+                               A7E9B7FD12D37EC400DA6239 /* sharedkstest.h */,
+                               A7E9B7FE12D37EC400DA6239 /* sharedkulczynski.cpp */,
+                               A7E9B7FF12D37EC400DA6239 /* sharedkulczynski.h */,
+                               A7E9B80012D37EC400DA6239 /* sharedkulczynskicody.cpp */,
+                               A7E9B80112D37EC400DA6239 /* sharedkulczynskicody.h */,
+                               A7E9B80212D37EC400DA6239 /* sharedlennon.cpp */,
+                               A7E9B80312D37EC400DA6239 /* sharedlennon.h */,
+                               A7E9B80612D37EC400DA6239 /* sharedmarczewski.cpp */,
+                               A7E9B80712D37EC400DA6239 /* sharedmarczewski.h */,
+                               A7E9B80812D37EC400DA6239 /* sharedmorisitahorn.cpp */,
+                               A7E9B80912D37EC400DA6239 /* sharedmorisitahorn.h */,
+                               A7E9B80A12D37EC400DA6239 /* sharednseqs.h */,
+                               A7E9B80B12D37EC400DA6239 /* sharedochiai.cpp */,
+                               A7E9B80C12D37EC400DA6239 /* sharedochiai.h */,
+                               A7E9B81512D37EC400DA6239 /* sharedsobs.cpp */,
+                               A7E9B81612D37EC400DA6239 /* sharedsobs.h */,
+                               A7E9B81712D37EC400DA6239 /* sharedsobscollectsummary.cpp */,
+                               A7E9B81812D37EC400DA6239 /* sharedsobscollectsummary.h */,
+                               A7E9B81912D37EC400DA6239 /* sharedsorabund.cpp */,
+                               A7E9B81A12D37EC400DA6239 /* sharedsorabund.h */,
+                               A7E9B81B12D37EC400DA6239 /* sharedsorclass.cpp */,
+                               A7E9B81C12D37EC400DA6239 /* sharedsorclass.h */,
+                               A7E9B81D12D37EC400DA6239 /* sharedsorest.cpp */,
+                               A7E9B81E12D37EC400DA6239 /* sharedsorest.h */,
+                               A7E9B81F12D37EC400DA6239 /* sharedthetan.cpp */,
+                               A7E9B82012D37EC400DA6239 /* sharedthetan.h */,
+                               A7E9B82112D37EC400DA6239 /* sharedthetayc.cpp */,
+                               A7E9B82212D37EC400DA6239 /* sharedthetayc.h */,
+                               A7E9B82512D37EC400DA6239 /* shen.cpp */,
+                               A7E9B82612D37EC400DA6239 /* shen.h */,
+                               A7E9B82912D37EC400DA6239 /* simpson.cpp */,
+                               A7E9B82A12D37EC400DA6239 /* simpson.h */,
+                               A7E9B82B12D37EC400DA6239 /* simpsoneven.cpp */,
+                               A7E9B82C12D37EC400DA6239 /* simpsoneven.h */,
+                               A7E9B83212D37EC400DA6239 /* smithwilson.cpp */,
+                               A7E9B83312D37EC400DA6239 /* smithwilson.h */,
+                               A7E9B83412D37EC400DA6239 /* sobs.h */,
+                               A7E9B83512D37EC400DA6239 /* soergel.cpp */,
+                               A7E9B83612D37EC400DA6239 /* soergel.h */,
+                               A7E9B83712D37EC400DA6239 /* solow.cpp */,
+                               A7E9B83812D37EC400DA6239 /* solow.h */,
+                               A7E9B83B12D37EC400DA6239 /* spearman.cpp */,
+                               A7E9B83C12D37EC400DA6239 /* spearman.h */,
+                               A7E9B83D12D37EC400DA6239 /* speciesprofile.cpp */,
+                               A7E9B83E12D37EC400DA6239 /* speciesprofile.h */,
+                               A7E9B84512D37EC400DA6239 /* structchi2.cpp */,
+                               A7E9B84612D37EC400DA6239 /* structchi2.h */,
+                               A7E9B84712D37EC400DA6239 /* structchord.cpp */,
+                               A7E9B84812D37EC400DA6239 /* structchord.h */,
+                               A7E9B84912D37EC400DA6239 /* structeuclidean.cpp */,
+                               A7E9B84A12D37EC400DA6239 /* structeuclidean.h */,
+                               A7E9B84B12D37EC400DA6239 /* structkulczynski.cpp */,
+                               A7E9B84C12D37EC400DA6239 /* structkulczynski.h */,
+                               A7E9B84D12D37EC400DA6239 /* structpearson.cpp */,
+                               A7E9B84E12D37EC400DA6239 /* structpearson.h */,
+                               A7E9B86112D37EC400DA6239 /* treecalculator.h */,
+                               A7E9B87012D37EC400DA6239 /* unweighted.cpp */,
+                               A7E9B87112D37EC400DA6239 /* unweighted.h */,
+                               A7E9B87212D37EC400DA6239 /* uvest.cpp */,
+                               A7E9B87312D37EC400DA6239 /* uvest.h */,
+                               A7E9B87C12D37EC400DA6239 /* weighted.cpp */,
+                               A7E9B87D12D37EC400DA6239 /* weighted.h */,
+                               A7E9B87F12D37EC400DA6239 /* whittaker.cpp */,
+                               A7E9B88012D37EC400DA6239 /* whittaker.h */,
+                       );
+                       name = calculators;
+                       sourceTree = "<group>";
+               };
+               A7E9BA4212D3960D00DA6239 /* containers */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7E9B65312D37EC300DA6239 /* alignment.cpp */,
+                               A7E9B65412D37EC300DA6239 /* alignment.hpp */,
+                               A7E9B65512D37EC300DA6239 /* alignmentcell.cpp */,
+                               A7E9B65612D37EC300DA6239 /* alignmentcell.hpp */,
+                               A7E9B65712D37EC300DA6239 /* alignmentdb.cpp */,
+                               A7E9B65812D37EC300DA6239 /* alignmentdb.h */,
+                               A7E9B66212D37EC300DA6239 /* blastalign.cpp */,
+                               A7E9B66312D37EC400DA6239 /* blastalign.hpp */,
+                               A7E9B66412D37EC400DA6239 /* blastdb.cpp */,
+                               A7E9B66512D37EC400DA6239 /* blastdb.hpp */,
+                               A7E9B6BD12D37EC400DA6239 /* database.cpp */,
+                               A7E9B6BE12D37EC400DA6239 /* database.hpp */,
+                               A7E9B6BF12D37EC400DA6239 /* datavector.hpp */,
+                               A7E9B6CD12D37EC400DA6239 /* distancedb.cpp */,
+                               A7E9B6CE12D37EC400DA6239 /* distancedb.hpp */,
+                               A7E9B6DE12D37EC400DA6239 /* fastamap.cpp */,
+                               A7E9B6DF12D37EC400DA6239 /* fastamap.h */,
+                               A7E9B6E812D37EC400DA6239 /* flowdata.h */,
+                               A7E9B6E712D37EC400DA6239 /* flowdata.cpp */,
+                               A7E9B6EE12D37EC400DA6239 /* fullmatrix.cpp */,
+                               A7E9B6EF12D37EC400DA6239 /* fullmatrix.h */,
+                               A7E9B71412D37EC400DA6239 /* groupmap.cpp */,
+                               A7E9B71512D37EC400DA6239 /* groupmap.h */,
+                               A7E9B73312D37EC400DA6239 /* kmer.cpp */,
+                               A7E9B73412D37EC400DA6239 /* kmer.hpp */,
+                               A7E9B73512D37EC400DA6239 /* kmerdb.cpp */,
+                               A7E9B73612D37EC400DA6239 /* kmerdb.hpp */,
+                               A7E9B73F12D37EC400DA6239 /* listvector.cpp */,
+                               A7E9B74012D37EC400DA6239 /* listvector.hpp */,
+                               A7E9B75F12D37EC400DA6239 /* nameassignment.cpp */,
+                               A7E9B76012D37EC400DA6239 /* nameassignment.hpp */,
+                               A7E9B77712D37EC400DA6239 /* ordervector.cpp */,
+                               A7E9B77812D37EC400DA6239 /* ordervector.hpp */,
+                               A7E9B79F12D37EC400DA6239 /* qualityscores.cpp */,
+                               A7E9B7A012D37EC400DA6239 /* qualityscores.h */,
+                               A7E9B7A312D37EC400DA6239 /* rabundvector.cpp */,
+                               A7E9B7A412D37EC400DA6239 /* rabundvector.hpp */,
+                               A7E9B7CB12D37EC400DA6239 /* reportfile.cpp */,
+                               A7E9B7CC12D37EC400DA6239 /* reportfile.h */,
+                               A7E9B7CF12D37EC400DA6239 /* sabundvector.cpp */,
+                               A7E9B7D012D37EC400DA6239 /* sabundvector.hpp */,
+                               A7E9B7DB12D37EC400DA6239 /* sequence.cpp */,
+                               A7E9B7DC12D37EC400DA6239 /* sequence.hpp */,
+                               A7E9B7DD12D37EC400DA6239 /* sequencedb.cpp */,
+                               A7E9B7DE12D37EC400DA6239 /* sequencedb.h */,
+                               A7E9B80412D37EC400DA6239 /* sharedlistvector.cpp */,
+                               A7E9B80512D37EC400DA6239 /* sharedlistvector.h */,
+                               A7E9B80D12D37EC400DA6239 /* sharedordervector.cpp */,
+                               A7E9B80E12D37EC400DA6239 /* sharedordervector.h */,
+                               A7E9B80F12D37EC400DA6239 /* sharedrabundfloatvector.cpp */,
+                               A7E9B81012D37EC400DA6239 /* sharedrabundfloatvector.h */,
+                               A7E9B81112D37EC400DA6239 /* sharedrabundvector.cpp */,
+                               A7E9B81212D37EC400DA6239 /* sharedrabundvector.h */,
+                               A7E9B81312D37EC400DA6239 /* sharedsabundvector.cpp */,
+                               A7E9B81412D37EC400DA6239 /* sharedsabundvector.h */,
+                               A7E9B83912D37EC400DA6239 /* sparsematrix.cpp */,
+                               A7E9B83A12D37EC400DA6239 /* sparsematrix.hpp */,
+                               A7E9B85F12D37EC400DA6239 /* tree.cpp */,
+                               A7E9B86012D37EC400DA6239 /* tree.h */,
+                               A7E9B86412D37EC400DA6239 /* treemap.cpp */,
+                               A7E9B86512D37EC400DA6239 /* treemap.h */,
+                               A7E9B86612D37EC400DA6239 /* treenode.cpp */,
+                               A7E9B86712D37EC400DA6239 /* treenode.h */,
                        );
                        name = containers;
                        sourceTree = "<group>";
                };
-               A7CB594511402F6E0010EB83 /* classifers */ = {
+               A7E9BA4512D3965600DA6239 /* chimera */ = {
+                       isa = PBXGroup;
+                       children = (
+                               A7E9B65C12D37EC300DA6239 /* bellerophon.cpp */,
+                               A7E9B65D12D37EC300DA6239 /* bellerophon.h */,
+                               A7E9B67412D37EC400DA6239 /* ccode.cpp */,
+                               A7E9B67512D37EC400DA6239 /* ccode.h */,
+                               A7E9B67812D37EC400DA6239 /* chimera.cpp */,
+                               A7E9B67912D37EC400DA6239 /* chimera.h */,
+                               A7E9B68012D37EC400DA6239 /* chimeracheckrdp.cpp */,
+                               A7E9B68112D37EC400DA6239 /* chimeracheckrdp.h */,
+                               A7E9B68412D37EC400DA6239 /* chimerarealigner.cpp */,
+                               A7E9B68512D37EC400DA6239 /* chimerarealigner.h */,
+                               A7E9B68812D37EC400DA6239 /* chimeraslayer.cpp */,
+                               A7E9B68912D37EC400DA6239 /* chimeraslayer.h */,
+                               A7E9B6C112D37EC400DA6239 /* decalc.cpp */,
+                               A7E9B6C212D37EC400DA6239 /* decalc.h */,
+                               A7E9B74612D37EC400DA6239 /* maligner.h */,
+                               A7E9B74512D37EC400DA6239 /* maligner.cpp */,
+                               A7E9B79312D37EC400DA6239 /* pintail.cpp */,
+                               A7E9B79412D37EC400DA6239 /* pintail.h */,
+                               A7E9B82E12D37EC400DA6239 /* slayer.cpp */,
+                               A7E9B82F12D37EC400DA6239 /* slayer.h */,
+                       );
+                       name = chimera;
+                       sourceTree = "<group>";
+               };
+               A7E9BA4B12D3966900DA6239 /* classifier */ = {
                        isa = PBXGroup;
                        children = (
-                               A7DA201B113FECD400BF472F /* classify.cpp */,
-                               A7DA201C113FECD400BF472F /* classify.h */,
-                               A7DA1FF7113FECD400BF472F /* bayesian.cpp */,
-                               A7DA1FF8113FECD400BF472F /* bayesian.h */,
-                               A7DA2089113FECD400BF472F /* knn.cpp */,
-                               A7DA208A113FECD400BF472F /* knn.h */,
-                               A7DA20C4113FECD400BF472F /* phylotree.cpp */,
-                               A7DA20C5113FECD400BF472F /* phylotree.h */,
-                               A76AAD02117F322B003D8DA1 /* phylosummary.h */,
-                               A76AAD03117F322B003D8DA1 /* phylosummary.cpp */,
-                               A7DA215C113FECD400BF472F /* taxonomyequalizer.cpp */,
-                               A7DA215D113FECD400BF472F /* taxonomyequalizer.h */,
+                               A7E9B65A12D37EC300DA6239 /* bayesian.cpp */,
+                               A7E9B65B12D37EC300DA6239 /* bayesian.h */,
+                               A7E9B68E12D37EC400DA6239 /* classify.cpp */,
+                               A7E9B68F12D37EC400DA6239 /* classify.h */,
+                               A7E9B73812D37EC400DA6239 /* knn.h */,
+                               A7E9B73712D37EC400DA6239 /* knn.cpp */,
+                               A7E9B78912D37EC400DA6239 /* phylodiversity.cpp */,
+                               A7E9B78A12D37EC400DA6239 /* phylodiversity.h */,
+                               A7E9B78D12D37EC400DA6239 /* phylosummary.cpp */,
+                               A7E9B78E12D37EC400DA6239 /* phylosummary.h */,
+                               A7E9B78F12D37EC400DA6239 /* phylotree.cpp */,
+                               A7E9B79012D37EC400DA6239 /* phylotree.h */,
+                               A7E9B85D12D37EC400DA6239 /* taxonomyequalizer.cpp */,
+                               A7E9B85E12D37EC400DA6239 /* taxonomyequalizer.h */,
                        );
-                       name = classifers;
+                       name = classifier;
                        sourceTree = "<group>";
                };
-               A7CB594A11402FB40010EB83 /* chimeras */ = {
+               A7E9BA4F12D398D700DA6239 /* clearcut */ = {
                        isa = PBXGroup;
                        children = (
-                               A7DA2011113FECD400BF472F /* chimera.cpp */,
-                               A7DA2012113FECD400BF472F /* chimera.h */,
-                               A7DA1FF9113FECD400BF472F /* bellerophon.cpp */,
-                               A7DA1FFA113FECD400BF472F /* bellerophon.h */,
-                               A7DA200D113FECD400BF472F /* ccode.cpp */,
-                               A7DA200E113FECD400BF472F /* ccode.h */,
-                               A7DA2013113FECD400BF472F /* chimeracheckrdp.cpp */,
-                               A7DA2014113FECD400BF472F /* chimeracheckrdp.h */,
-                               A7DA2015113FECD400BF472F /* chimerarealigner.cpp */,
-                               A7DA2016113FECD400BF472F /* chimerarealigner.h */,
-                               A7DA2019113FECD400BF472F /* chimeraslayer.cpp */,
-                               A7DA201A113FECD400BF472F /* chimeraslayer.h */,
-                               A7DA2038113FECD400BF472F /* decalc.cpp */,
-                               A7DA2039113FECD400BF472F /* decalc.h */,
-                               A7DA2095113FECD400BF472F /* maligner.cpp */,
-                               A7DA2096113FECD400BF472F /* maligner.h */,
-                               A7DA20C8113FECD400BF472F /* pintail.cpp */,
-                               A7DA20C9113FECD400BF472F /* pintail.h */,
-                               A7DA2145113FECD400BF472F /* slayer.cpp */,
-                               A7DA2146113FECD400BF472F /* slayer.h */,
+                               A7E9B69412D37EC400DA6239 /* clearcut.cpp */,
+                               A7E9B69512D37EC400DA6239 /* clearcut.h */,
+                               A7E9B6B312D37EC400DA6239 /* common.h */,
+                               A7E9B6CF12D37EC400DA6239 /* distclearcut.cpp */,
+                               A7E9B6D012D37EC400DA6239 /* distclearcut.h */,
+                               A7E9B6D312D37EC400DA6239 /* dmat.cpp */,
+                               A7E9B6D412D37EC400DA6239 /* dmat.h */,
+                               A7E9B6DC12D37EC400DA6239 /* fasta.cpp */,
+                               A7E9B6DD12D37EC400DA6239 /* fasta.h */,
+                               A7E9B6FD12D37EC400DA6239 /* getopt_long.h */,
+                               A7E9B6FC12D37EC400DA6239 /* getopt_long.cpp */,
                        );
-                       name = chimeras;
+                       name = clearcut;
                        sourceTree = "<group>";
                };
-               A7CB5953114033220010EB83 /* read */ = {
+               A7E9BA5312D39A5E00DA6239 /* read */ = {
                        isa = PBXGroup;
                        children = (
-                               A7DA2051113FECD400BF472F /* formatcolumn.cpp */,
-                               A7DA2052113FECD400BF472F /* formatcolumn.h */,
-                               A7DA2053113FECD400BF472F /* formatmatrix.h */,
-                               A7DA2054113FECD400BF472F /* formatphylip.cpp */,
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+                               A7E9B98D12D37EC400DA6239 /* weighted.cpp in Sources */,
+                               A7E9B98E12D37EC400DA6239 /* weightedlinkage.cpp in Sources */,
+                               A7E9B98F12D37EC400DA6239 /* whittaker.cpp in Sources */,
+                       );
+                       runOnlyForDeploymentPostprocessing = 0;
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+/* End PBXSourcesBuildPhase section */
+
 /* Begin XCBuildConfiguration section */
-               1DEB919108733D9F0010E9CD /* Release */ = {
+               1DEB928608733DD80010E9CD /* Debug */ = {
                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               COPY_PHASE_STRIP = YES;
-                               GCC_ENABLE_FIX_AND_CONTINUE = NO;
-                               OTHER_CFLAGS = "";
-                               OTHER_LDFLAGS = "";
+                               ALWAYS_SEARCH_USER_PATHS = NO;
+                               COPY_PHASE_STRIP = NO;
+                               GCC_DYNAMIC_NO_PIC = NO;
+                               GCC_ENABLE_FIX_AND_CONTINUE = YES;
+                               GCC_MODEL_TUNING = G5;
+                               GCC_OPTIMIZATION_LEVEL = 0;
+                               INSTALL_PATH = /usr/local/bin;
+                               PRODUCT_NAME = mothur;
+                       };
+                       name = Debug;
+               };
+               1DEB928708733DD80010E9CD /* Release */ = {
+                       isa = XCBuildConfiguration;
+                       buildSettings = {
+                               ALWAYS_SEARCH_USER_PATHS = NO;
+                               DEBUG_INFORMATION_FORMAT = "dwarf-with-dsym";
+                               DEPLOYMENT_LOCATION = YES;
+                               GCC_MODEL_TUNING = G5;
+                               GCC_WARN_UNUSED_VALUE = YES;
+                               INSTALL_PATH = ./;
                                PRODUCT_NAME = mothur;
-                               ZERO_LINK = NO;
                        };
                        name = Release;
                };
-               1DEB919508733D9F0010E9CD /* Release */ = {
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                        isa = XCBuildConfiguration;
                        buildSettings = {
-                               ARCHS = (
-                                       ppc,
-                                       i386,
+                               ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
+                               DEPLOYMENT_LOCATION = NO;
+                               GCC_C_LANGUAGE_STANDARD = gnu99;
+                               GCC_OPTIMIZATION_LEVEL = 0;
+                               GCC_PREPROCESSOR_DEFINITIONS = (
+                                       "MOTHUR_FILES=\"\\\"../release\\\"\"",
+                                       "VERSION=\"\\\"1.15.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
                                );
                                GCC_WARN_ABOUT_RETURN_TYPE = YES;
                                GCC_WARN_UNUSED_VARIABLE = YES;
-                               LINK_WITH_STANDARD_LIBRARIES = YES;
+                               INSTALL_PATH = "";
+                               ONLY_ACTIVE_ARCH = YES;
+                               OTHER_CPLUSPLUSFLAGS = (
+                                       "-DUSE_READLINE",
+                                       "-DBIT_VERSION",
+                                       "$(OTHER_CFLAGS)",
+                               );
+                               OTHER_LDFLAGS = (
+                                       "-lncurses",
+                                       "-lreadline",
+                               );
+                               PREBINDING = NO;
+                               SDKROOT = macosx10.5;
+                       };
+                       name = Debug;
+               };
+               1DEB928B08733DD80010E9CD /* Release */ = {
+                       isa = XCBuildConfiguration;
+                       buildSettings = {
+                               ARCHS = "$(ARCHS_STANDARD_32_64_BIT)";
+                               DEPLOYMENT_LOCATION = NO;
+                               GCC_C_LANGUAGE_STANDARD = gnu99;
+                               GCC_PREPROCESSOR_DEFINITIONS = (
+                                       "MOTHUR_FILES=\"\\\"../release\\\"\"",
+                                       "VERSION=\"\\\"1.15.0\\\"\"",
+                                       "RELEASE_DATE=\"\\\"12/10/2010\\\"\"",
+                               );
+                               GCC_WARN_ABOUT_MISSING_NEWLINE = YES;
+                               GCC_WARN_ABOUT_RETURN_TYPE = YES;
+                               GCC_WARN_MISSING_PARENTHESES = YES;
+                               GCC_WARN_MULTIPLE_DEFINITION_TYPES_FOR_SELECTOR = YES;
+                               GCC_WARN_UNUSED_FUNCTION = YES;
+                               GCC_WARN_UNUSED_PARAMETER = YES;
+                               GCC_WARN_UNUSED_VALUE = YES;
+                               GCC_WARN_UNUSED_VARIABLE = YES;
+                               INSTALL_PATH = "";
+                               OTHER_CPLUSPLUSFLAGS = (
+                                       "-DUSE_READLINE",
+                                       "-DBIT_VERSION",
+                                       "$(OTHER_CFLAGS)",
+                               );
+                               OTHER_LDFLAGS = (
+                                       "-lncurses",
+                                       "-lreadline",
+                               );
                                PREBINDING = NO;
-                               SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.6.sdk";
+                               SDKROOT = macosx10.5;
                        };
                        name = Release;
                };
 /* End XCBuildConfiguration section */
 
 /* Begin XCConfigurationList section */
-               1DEB918F08733D9F0010E9CD /* Build configuration list for PBXLegacyTarget "mothur" */ = {
+               1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
-                               1DEB919108733D9F0010E9CD /* Release */,
+                               1DEB928608733DD80010E9CD /* Debug */,
+                               1DEB928708733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB919308733D9F0010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
-                               1DEB919508733D9F0010E9CD /* Release */,
+                               1DEB928A08733DD80010E9CD /* Debug */,
+                               1DEB928B08733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;

diff --git a/bellerophon.cpp b/bellerophon.cpp
index 761d291da566aa1495b4f4a8e75079f1a619a617..6e1e242f9634b41efbc38bd3ff9e1584be850d03 100644 (file)
--- a/bellerophon.cpp
+++ b/bellerophon.cpp
@@ -535,7 +535,7 @@ int Bellerophon::createSparseMatrix(int startSeq, int endSeq, SparseMatrix* spar
 int Bellerophon::generatePreferences(vector<SeqMap> left, vector<SeqMap> right, int mid){
        try {
                
-               float dme = 0.0;
+               //float dme = 0.0;
                SeqMap::iterator itR;
                SeqMap::iterator itL;
                

diff --git a/clustersplitcommand.cpp b/clustersplitcommand.cpp
index 85c70f04127b4ae63ddf1f16f6e8adb2fea39e9c..5998726fe3e4d48523ac6a771a9609dae328f739 100644 (file)
--- a/clustersplitcommand.cpp
+++ b/clustersplitcommand.cpp
@@ -538,7 +538,6 @@ int ClusterSplitCommand::execute(){
                                        
                                        //for each file group figure out which process will complete it
                                        //want to divide the load intelligently so the big files are spread between processes
-                                       int count = 1;
                                        for (int i = 0; i < distName.size(); i++) { 
                                                int processToAssign = (i+1) % processors; 
                                                if (processToAssign == 0) { processToAssign = processors; }
@@ -991,9 +990,7 @@ vector<string> ClusterSplitCommand::cluster(vector< map<string, string> > distNa
                        m->openOutputFile(fileroot+ tag + ".list",      listFile);
                
                        listFileNames.push_back(fileroot+ tag + ".list");
-               
-                       time_t estart = time(NULL);
-                       
+                               
                        float previousDist = 0.00000;
                        float rndPreviousDist = 0.00000;
                        

diff --git a/flowdata.cpp b/flowdata.cpp
index a172a03337303f287c64ed0f8e7352cdfde3db57..eb6f9bfec3a88b05bf2dcd03a751b01b320430d0 100644 (file)
--- a/flowdata.cpp
+++ b/flowdata.cpp
@@ -68,7 +68,7 @@ bool FlowData::getNext(ifstream& flowFile){
 void FlowData::updateEndFlow(){
        try{
                
-               int currLength = 0;
+               //int currLength = 0;
                float maxIntensity = (float) maxHomoP + 0.49;
                
                int deadSpot = 0;

diff --git a/getlineagecommand.cpp b/getlineagecommand.cpp
index 8a825a1ca76c077cade0e6aecd078eb3fa72ea38..4231435e556f205b753985bacca8d418b0d07c2c 100644 (file)
--- a/getlineagecommand.cpp
+++ b/getlineagecommand.cpp
@@ -542,7 +542,7 @@ int GetLineageCommand::readTax(){
                m->openInputFile(taxfile, in);
                string name, tax;
                
-               bool wroteSomething = false;
+               //bool wroteSomething = false;
                
                bool taxonsHasConfidence = false;
                vector< map<string, int> > searchTaxons;

diff --git a/mothurout.cpp b/mothurout.cpp
index 54cf25d891e4528b1a6c1f08bc350a58b8aeb9e6..27b36ce5ff83dceadeb77e84045caef94d5168c9 100644 (file)
--- a/mothurout.cpp
+++ b/mothurout.cpp
@@ -927,7 +927,7 @@ vector<unsigned long int> MothurOut::setFilePosFasta(string filename, int& num)
                        
                        in.seekg(size);
                
-                       while(char c = in.get()){
+                       while(in.get()){
                                if(in.eof())            {       break;  }
                                else                            {       size++; }
                        }

diff --git a/seqerrorcommand.cpp b/seqerrorcommand.cpp
index 58140ab3554a0e406c041cf483e15953b453a7be..fe6d4ddf8699e03eab527033f763692288b44072 100644 (file)
--- a/seqerrorcommand.cpp
+++ b/seqerrorcommand.cpp
@@ -355,9 +355,7 @@ int SeqErrorCommand::execute(){
                        
                }
                queryFile.close();
-               
-               int total = 0;
-               
+                               
                if(qualFileName != "" && reportFileName != ""){
                        string errorQualityFileName = queryFileName.substr(0,queryFileName.find_last_of('.')) + ".error.quality";
                        ofstream errorQualityFile;

diff --git a/trimflowscommand.cpp b/trimflowscommand.cpp
index 3b21d317b2c8f82729418516ad87d23c31392ed0..b098f8f68559c468b48a1fef4dbd34ecc7504db3 100644 (file)
--- a/trimflowscommand.cpp
+++ b/trimflowscommand.cpp
@@ -775,7 +775,6 @@ int TrimFlowsCommand::stripForward(Sequence& seq, int& group){
                                oligo = oligo.substr(0,alnLength);
                                temp = temp.substr(0,alnLength);
                                
-                               int newStart=0;
                                int numDiff = countDiffs(oligo, temp);
                                
                                if(numDiff < minDiff){

diff --git a/weighted.cpp b/weighted.cpp
index 1ce6230df933eab46bee132a76ec32c2c4e9a666..24adbba9de929382c8bbcaa3efc2272365c73f24 100644 (file)
--- a/weighted.cpp
+++ b/weighted.cpp
@@ -73,7 +73,6 @@ EstOutput Weighted::createProcesses(Tree* t, vector< vector<string> > namesOfGro
        try {
 #if defined (__APPLE__) || (__MACH__) || (linux) || (__linux)
                int process = 1;
-               int num = 0;
                vector<int> processIDS;
                
                EstOutput results;
@@ -204,9 +203,7 @@ EstOutput Weighted::driver(Tree* t, vector< vector<string> > namesOfGroupCombos,
                for (int h = start; h < (start+num); h++) {     
                        //report progress
                        m->mothurOut("Processing combo: " + toString(h)); m->mothurOutEndLine();
-                       
-                       int numLeaves = t->getNumLeaves();
-                       
+                                               
                        string groupA = namesOfGroupCombos[h][0]; 
                        string groupB = namesOfGroupCombos[h][1];