changes to trim.flows command

[mothur.git] / Mothur.xcodeproj / project.pbxproj

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index 21dbf8dfbb074de24a0b70e523bd95e56d414695..9216cc134d2b406308a78eca23acb81648742e89 100644 (file)
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
@@ -3,713 +3,1012 @@
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+                               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 */,
+                               A7FC480C12D788F20055BC5C /* linearalgebra.h */,
+                               A7FC480D12D788F20055BC5C /* linearalgebra.cpp */,
+                               A7E9BA5612D39BD800DA6239 /* metastats */,
+                               A7E9B75B12D37EC400DA6239 /* mothur.cpp */,
+                               A7E9B75C12D37EC400DA6239 /* mothur.h */,
+                               A7E9B75D12D37EC400DA6239 /* mothurout.cpp */,
+                               A7E9B75E12D37EC400DA6239 /* mothurout.h */,
+                               A7E9B76112D37EC400DA6239 /* nast.cpp */,
+                               A7E9B76212D37EC400DA6239 /* nast.hpp */,
+                               A7E9B76312D37EC400DA6239 /* nastreport.cpp */,
+                               A7E9B76412D37EC400DA6239 /* nastreport.hpp */,
+                               A7E9B76712D37EC400DA6239 /* noalign.cpp */,
+                               A7E9B76812D37EC400DA6239 /* noalign.hpp */,
+                               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 */,
+                               7E6BE10812F710D8007ADDBE /* refchimeratest.h */,
+                               7E6BE10912F710D8007ADDBE /* refchimeratest.cpp */,
+                               A7E9BA5312D39A5E00DA6239 /* read */,
+                               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 = Source;
                        sourceTree = "<group>";
@@ -717,392 +1016,567 @@
                1AB674ADFE9D54B511CA2CBB /* Products */ = {
                        isa = PBXGroup;
                        children = (
-                               8DD76F6C0486A84900D96B5E /* mothur */,
+                               8DD76FB20486AB0100D96B5E /* Mothur */,
                        );
                        name = Products;
                        sourceTree = "<group>";
                };
-               374F2FE81006346600E97C66 /* chimera */ = {
+               A7E9BA3812D3956100DA6239 /* commands */ = {
                        isa = PBXGroup;
                        children = (
-                               374F2FD51006320200E97C66 /* chimera.h */,
-                               372095C1103196D70004D347 /* chimera.cpp */,
-                               374F2FE9100634B600E97C66 /* bellerophon.h */,
-                               374F2FEA100634B600E97C66 /* bellerophon.cpp */,
-                               A75B887C104C16860083C454 /* ccode.h */,
-                               A75B887B104C16860083C454 /* ccode.cpp */,
-                               A7283FF61056CAE100D0CC69 /* chimeracheckrdp.h */,
-                               A7283FF71056CAE100D0CC69 /* chimeracheckrdp.cpp */,
-                               A7B04491106CC3E60046FC83 /* chimeraslayer.h */,
-                               A7B04492106CC3E60046FC83 /* chimeraslayer.cpp */,
-                               372A55531017922B00C5194B /* decalc.h */,
-                               372A55541017922B00C5194B /* decalc.cpp */,
-                               A7E4A822106A9AD700688F62 /* maligner.h */,
-                               A7E4A823106A9AD700688F62 /* maligner.cpp */,
-                               374F301110063B6F00E97C66 /* pintail.h */,
-                               374F301210063B6F00E97C66 /* pintail.cpp */,
-                               A7B0450C106CEEC90046FC83 /* slayer.h */,
-                               A7B0450D106CEEC90046FC83 /* slayer.cpp */,
+                               A7E9B6AE12D37EC400DA6239 /* command.hpp */,
+                               A7E9B65112D37EC300DA6239 /* aligncommand.cpp */,
+                               A7E9B65212D37EC300DA6239 /* aligncommand.h */,
+                               A7A61F2B130062E000E05B6B /* amovacommand.h */,
+                               A7A61F2C130062E000E05B6B /* amovacommand.cpp */,
+                               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 */,
+                               A75790571301749D00A30DAB /* homovacommand.h */,
+                               A75790581301749D00A30DAB /* homovacommand.cpp */,
+                               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 */,
+                               A71FE12A12EDF72400963CA7 /* mergegroupscommand.h */,
+                               A71FE12B12EDF72400963CA7 /* mergegroupscommand.cpp */,
+                               A7E9B75712D37EC400DA6239 /* metastatscommand.cpp */,
+                               A7E9B75812D37EC400DA6239 /* metastatscommand.h */,
+                               A7E9B75912D37EC400DA6239 /* mgclustercommand.cpp */,
+                               A7E9B75A12D37EC400DA6239 /* mgclustercommand.h */,
+                               A7E9B76A12D37EC400DA6239 /* nocommands.h */,
+                               A7E9B76912D37EC400DA6239 /* nocommands.cpp */,
+                               A7E9B76B12D37EC400DA6239 /* normalizesharedcommand.cpp */,
+                               A7E9B76C12D37EC400DA6239 /* normalizesharedcommand.h */,
+                               A713EBEB12DC7C5E000092AC /* nmdscommand.h */,
+                               A713EBEC12DC7C5E000092AC /* nmdscommand.cpp */,
+                               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 */,
+                               A7FC486512D795D60055BC5C /* pcacommand.h */,
+                               A7FC486612D795D60055BC5C /* pcacommand.cpp */,
+                               A7E9B78712D37EC400DA6239 /* pcoacommand.cpp */,
+                               A7E9B78812D37EC400DA6239 /* pcoacommand.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 */,
+                               A727864212E9E28C00F86ABA /* removerarecommand.h */,
+                               A727864312E9E28C00F86ABA /* removerarecommand.cpp */,
+                               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 = chimera;
+                       name = commands;
                        sourceTree = "<group>";
                };
-               3796441D0FB9B9650081FDB6 /* read */ = {
+               A7E9BA3F12D395F700DA6239 /* calculators */ = {
                        isa = PBXGroup;
                        children = (
-                               A7D86C6A10FE084300865661 /* formatmatrix.h */,
-                               A7D86C7B10FE09AB00865661 /* formatcolumn.h */,
-                               A7D86C7C10FE09AB00865661 /* formatcolumn.cpp */,
-                               A7D86C8A10FE09FE00865661 /* formatphylip.h */,
-                               A7D86C8B10FE09FE00865661 /* formatphylip.cpp */,
-                               A727E84810D14568001A8432 /* readblast.h */,
-                               A727E84910D14568001A8432 /* readblast.cpp */,
-                               A751ACE81098B283003D0911 /* readcluster.h */,
-                               A751ACE91098B283003D0911 /* readcluster.cpp */,
-                               375AA1340F9E433D008EF9B8 /* readcolumn.h */,
-                               375AA1330F9E433D008EF9B8 /* readcolumn.cpp */,
-                               37D928130F21331F001D4494 /* readmatrix.hpp */,
-                               375AA1360F9E433D008EF9B8 /* readotu.h */,
-                               375AA1350F9E433D008EF9B8 /* readotu.cpp */,
-                               375AA1380F9E433D008EF9B8 /* readphylip.h */,
-                               375AA1370F9E433D008EF9B8 /* readphylip.cpp */,
-                               37AD4DC80F28F3DD00AA2D49 /* readtree.h */,
-                               37AD4DC90F28F3DD00AA2D49 /* readtree.cpp */,
+                               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 = read;
+                       name = calculators;
                        sourceTree = "<group>";
                };
-               37D928A60F2133C0001D4494 /* calculators */ = {
+               A7E9BA4212D3960D00DA6239 /* containers */ = {
                        isa = PBXGroup;
                        children = (
-                               37D927BE0F21331F001D4494 /* calculator.h */,
-                               37D927BD0F21331F001D4494 /* calculator.cpp */,
-                               3792948D0F2E271100B9034A /* treecalculator.h */,
-                               37D927B90F21331F001D4494 /* ace.h */,
-                               37D927B80F21331F001D4494 /* ace.cpp */,
-                               EB1216860F619B83004A865F /* bergerparker.h */,
-                               EB1216870F619B83004A865F /* bergerparker.cpp */,
-                               373C69950FC1E63600137ACD /* boneh.h */,
-                               373C69940FC1E63600137ACD /* boneh.cpp */,
-                               37D927BC0F21331F001D4494 /* bootstrap.h */,
-                               37D927BB0F21331F001D4494 /* bootstrap.cpp */,
-                               EB1216E30F61ACFB004A865F /* bstick.h */,
-                               EB1216E40F61ACFB004A865F /* bstick.cpp */,
-                               37D927C00F21331F001D4494 /* chao1.h */,
-                               37D927BF0F21331F001D4494 /* chao1.cpp */,
-                               7EC3D4510FA0FFF900338DA5 /* coverage.h */,
-                               7EC3D4500FA0FFF900338DA5 /* coverage.cpp */,
-                               37C753DF0FB3492400DBD02E /* dist.h */,
-                               37C753F00FB34AE800DBD02E /* eachgapdist.h */,
-                               37C753F40FB34C0300DBD02E /* eachgapignore.h */,
-                               373C69960FC1E63600137ACD /* efron.cpp */,
-                               373C69970FC1E63600137ACD /* efron.h */,
-                               379D3D6B0FF917F40068C1C0 /* filters.h */,
-                               EB9303F70F53517300E8EF26 /* geom.h */,
-                               EB9303F80F53517300E8EF26 /* geom.cpp */,
-                               378C1AF10FB0644D004D63F5 /* goodscoverage.h */,
-                               378C1AF00FB0644D004D63F5 /* goodscoverage.cpp */,
-                               37C753ED0FB34A5700DBD02E /* ignoregaps.h */,
-                               37D927E80F21331F001D4494 /* jackknife.h */,
-                               37D927E70F21331F001D4494 /* jackknife.cpp */,
-                               EB9303E90F534D9400E8EF26 /* logsd.h */,
-                               EB9303EA0F534D9400E8EF26 /* logsd.cpp */,
-                               375873F90F7D64AB0040F377 /* nseqs.h */,
-                               37D927F50F21331F001D4494 /* npshannon.h */,
-                               37D927F40F21331F001D4494 /* npshannon.cpp */,
-                               37C753F10FB34B4700DBD02E /* onegapdist.h */,
-                               37C753F30FB34BBF00DBD02E /* onegapignore.h */,
-                               379294880F2E258500B9034A /* parsimony.h */,
-                               379294890F2E258500B9034A /* parsimony.cpp */,
-                               EB6E68170F5F1C780044E17B /* qstat.h */,
-                               EB6E68180F5F1C780044E17B /* qstat.cpp */,
-                               37D928020F21331F001D4494 /* rarecalc.h */,
-                               37D928010F21331F001D4494 /* rarecalc.cpp */,
-                               37D9281F0F21331F001D4494 /* shannon.h */,
-                               37D9281E0F21331F001D4494 /* shannon.cpp */,
-                               37D928230F21331F001D4494 /* sharedace.h */,
-                               37D928220F21331F001D4494 /* sharedace.cpp */,
-                               37519A690F80E6EB00FED5E8 /* sharedanderbergs.h */,
-                               37519A6A0F80E6EB00FED5E8 /* sharedanderbergs.cpp */,
-                               7EC3D4520FA0FFF900338DA5 /* sharedanderberg.h */,
-                               375873FB0F7D64DA0040F377 /* sharedbraycurtis.h */,
-                               375873FC0F7D64DA0040F377 /* sharedbraycurtis.cpp */,
-                               37D928250F21331F001D4494 /* sharedchao1.h */,
-                               37D928240F21331F001D4494 /* sharedchao1.cpp */,
-                               37D928290F21331F001D4494 /* sharedjabund.h */,
-                               37D928280F21331F001D4494 /* sharedjabund.cpp */,
-                               378C1B000FB0644D004D63F5 /* sharedjackknife.h */,
-                               378C1AFF0FB0644D004D63F5 /* sharedjackknife.cpp */,
-                               37D9282B0F21331F001D4494 /* sharedjclass.h */,
-                               37D9282A0F21331F001D4494 /* sharedjclass.cpp */,
-                               37D9282D0F21331F001D4494 /* sharedjest.h */,
-                               37D9282C0F21331F001D4494 /* sharedjest.cpp */,
-                               EB1217210F61C9AC004A865F /* sharedkstest.h */,
-                               EB1217220F61C9AC004A865F /* sharedkstest.cpp */,
-                               375874000F7D64EF0040F377 /* sharedkulczynski.h */,
-                               375873FE0F7D64EF0040F377 /* sharedkulczynski.cpp */,
-                               375874030F7D64EF0040F377 /* sharedkulczynskicody.h */,
-                               375874020F7D64EF0040F377 /* sharedkulczynskicody.cpp */,
-                               375874010F7D64EF0040F377 /* sharedlennon.h */,
-                               375873FF0F7D64EF0040F377 /* sharedlennon.cpp */,
-                               378C1B020FB0644D004D63F5 /* sharedmarczewski.h */,
-                               378C1B010FB0644D004D63F5 /* sharedmarczewski.cpp */,
-                               375874070F7D64FC0040F377 /* sharedmorisitahorn.h */,
-                               375874080F7D64FC0040F377 /* sharedmorisitahorn.cpp */,
-                               375874090F7D64FC0040F377 /* sharedochiai.h */,
-                               3758740B0F7D64FC0040F377 /* sharedochiai.cpp */,
-                               3758740A0F7D64FC0040F377 /* sharednseqs.h */,
-                               37D928350F21331F001D4494 /* sharedsobs.h */,
-                               37D928340F21331F001D4494 /* sharedsobs.cpp */,
-                               37AFC71D0F445386005F492D /* sharedsobscollectsummary.h */,
-                               37AFC71E0F445386005F492D /* sharedsobscollectsummary.cpp */,
-                               37D928370F21331F001D4494 /* sharedsorabund.h */,
-                               37D928360F21331F001D4494 /* sharedsorabund.cpp */,
-                               37D928390F21331F001D4494 /* sharedsorclass.h */,
-                               37D928380F21331F001D4494 /* sharedsorclass.cpp */,
-                               37D9283B0F21331F001D4494 /* sharedsorest.h */,
-                               37D9283A0F21331F001D4494 /* sharedsorest.cpp */,
-                               37D9283D0F21331F001D4494 /* sharedthetan.h */,
-                               37D9283C0F21331F001D4494 /* sharedthetan.cpp */,
-                               37D9283F0F21331F001D4494 /* sharedthetayc.h */,
-                               37D9283E0F21331F001D4494 /* sharedthetayc.cpp */,
-                               EB72FE250FC1F5CA0051AC11 /* shen.h */,
-                               EB72FE240FC1F5CA0051AC11 /* shen.cpp */,
-                               37D928410F21331F001D4494 /* simpson.h */,
-                               37D928400F21331F001D4494 /* simpson.cpp */,
-                               37D928430F21331F001D4494 /* sobs.h */,
-                               373C69980FC1E63600137ACD /* solow.cpp */,
-                               373C69990FC1E63600137ACD /* solow.h */,
-                               374610810F40652400460C57 /* unweighted.h */,
-                               374610820F40652400460C57 /* unweighted.cpp */,
-                               37D9284E0F21331F001D4494 /* uvest.h */,
-                               37D9284D0F21331F001D4494 /* uvest.cpp */,
-                               3746107C0F4064D100460C57 /* weighted.h */,
-                               3746107D0F4064D100460C57 /* weighted.cpp */,
-                               7EC3D4540FA0FFF900338DA5 /* whittaker.h */,
-                               7EC3D4530FA0FFF900338DA5 /* whittaker.cpp */,
+                               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 = calculators;
+                       name = containers;
                        sourceTree = "<group>";
                };
-               37D928A90F2133E5001D4494 /* commands */ = {
+               A7E9BA4512D3965600DA6239 /* chimera */ = {
                        isa = PBXGroup;
                        children = (
-                               37D927CD0F21331F001D4494 /* command.hpp */,
-                               378DC5CD0FBDE1C8003B8607 /* aligncommand.h */,
-                               378DC5CE0FBDE1C8003B8607 /* aligncommand.cpp */,
-                               37C1D9710F86506E0059E3F0 /* binsequencecommand.h */,
-                               37C1D9720F86506E0059E3F0 /* binsequencecommand.cpp */,
-                               21DDC0190F97A8FE0060691C /* bootstrapsharedcommand.h */,
-                               21DDC01A0F97A8FE0060691C /* bootstrapsharedcommand.cpp */,
-                               37D927C40F21331F001D4494 /* clustercommand.h */,
-                               37D927C30F21331F001D4494 /* clustercommand.cpp */,
-                               37D927C80F21331F001D4494 /* collectcommand.h */,
-                               37D927C70F21331F001D4494 /* collectcommand.cpp */,
-                               37D927CC0F21331F001D4494 /* collectsharedcommand.h */,
-                               37D927CB0F21331F001D4494 /* collectsharedcommand.cpp */,
-                               377326640FAF16E0007ABB8B /* consensuscommand.h */,
-                               377326630FAF16E0007ABB8B /* consensuscommand.cpp */,
-                               379D3D4F0FF90E090068C1C0 /* chimeraseqscommand.h */,
-                               379D3D500FF90E090068C1C0 /* chimeraseqscommand.cpp */,
-                               A7861476109F5FA00010AAAF /* classifyseqscommand.h */,
-                               A7861477109F5FA00010AAAF /* classifyseqscommand.cpp */,
-                               37B28F660F27590100808A62 /* deconvolutecommand.h */,
-                               37B28F670F27590100808A62 /* deconvolutecommand.cpp */,
-                               37C753CC0FB3415200DBD02E /* distancecommand.h */,
-                               37C753CD0FB3415200DBD02E /* distancecommand.cpp */,
-                               378C1AEF0FB0644D004D63F5 /* filterseqscommand.h */,
-                               378C1AEE0FB0644D004D63F5 /* filterseqscommand.cpp */,
-                               A70B53A50F4CD7AD0064797E /* getgroupcommand.h */,
-                               A70B53A40F4CD7AD0064797E /* getgroupcommand.cpp */,
-                               A70B53A70F4CD7AD0064797E /* getlabelcommand.h */,
-                               A70B53A60F4CD7AD0064797E /* getlabelcommand.cpp */,
-                               A73329CD1083B3B3003B10C5 /* getlistcountcommand.h */,
-                               A73329CE1083B3B3003B10C5 /* getlistcountcommand.cpp */,
-                               370B88050F8A4EE4005AB382 /* getoturepcommand.h */,
-                               370B88060F8A4EE4005AB382 /* getoturepcommand.cpp */,
-                               3749273D0FD5956B0031C06B /* getrabundcommand.h */,
-                               3749273E0FD5956B0031C06B /* getrabundcommand.cpp */,
-                               3749271B0FD58C840031C06B /* getsabundcommand.h */,
-                               3749271C0FD58C840031C06B /* getsabundcommand.cpp */,
-                               37B73CA41004D89A008C4B41 /* getseqscommand.h */,
-                               37B73CA51004D89A008C4B41 /* getseqscommand.cpp */,
-                               A7E4A781106913F900688F62 /* getsharedotucommand.h */,
-                               A7E4A782106913F900688F62 /* getsharedotucommand.cpp */,
-                               A729ACCE10848E6100139801 /* hclustercommand.h */,
-                               A729ACCF10848E6100139801 /* hclustercommand.cpp */,
-                               375873F10F7D64800040F377 /* heatmapcommand.h */,
-                               375873F00F7D64800040F377 /* heatmapcommand.cpp */,
-                               378598640FDD497000EF9D03 /* heatmapsimcommand.h */,
-                               378598650FDD497000EF9D03 /* heatmapsimcommand.cpp */,
-                               37D927E40F21331F001D4494 /* helpcommand.h */,
-                               37D927E30F21331F001D4494 /* helpcommand.cpp */,
-                               375873F40F7D648F0040F377 /* libshuffcommand.h */,
-                               375873F30F7D648F0040F377 /* libshuffcommand.cpp */,
-                               37B73C741004BEFD008C4B41 /* listseqscommand.h */,
-                               37B73C751004BEFD008C4B41 /* listseqscommand.cpp */,
-                               21E859D60FC4632E005E1A48 /* matrixoutputcommand.h */,
-                               21E859D70FC4632E005E1A48 /* matrixoutputcommand.cpp */,
-                               7E5A17AD0FE57292003C6A03 /* mergefilecommand.h */,
-                               7E5A17AE0FE57292003C6A03 /* mergefilecommand.cpp */,
-                               A7E0AAB410D2886D00CF407B /* mgclustercommand.h */,
-                               A7E0AAB510D2886D00CF407B /* mgclustercommand.cpp */,
-                               375873F70F7D649C0040F377 /* nocommands.h */,
-                               375873F60F7D649C0040F377 /* nocommands.cpp */,
-                               A704E8A11106045D00870157 /* otuhierarchycommand.h */,
-                               A704E8A21106045D00870157 /* otuhierarchycommand.cpp */,
-                               3792946E0F2E191800B9034A /* parsimonycommand.h */,
-                               3792946F0F2E191800B9034A /* parsimonycommand.cpp */,
-                               A7D176CD10F2558500159497 /* pcacommand.h */,
-                               A7D176CE10F2558500159497 /* pcacommand.cpp */,
-                               A773808E10B6EFD1002A6A61 /* phylotypecommand.h */,
-                               A773808F10B6EFD1002A6A61 /* phylotypecommand.cpp */,
-                               A7027F2610DFF86D00BF45FE /* preclustercommand.h */,
-                               A7027F2710DFF86D00BF45FE /* preclustercommand.cpp */,
-                               37D927FE0F21331F001D4494 /* quitcommand.h */,
-                               37D927FD0F21331F001D4494 /* quitcommand.cpp */,
-                               37D928080F21331F001D4494 /* rarefactcommand.h */,
-                               37D928070F21331F001D4494 /* rarefactcommand.cpp */,
-                               37D9280B0F21331F001D4494 /* rarefactsharedcommand.h */,
-                               37D9280A0F21331F001D4494 /* rarefactsharedcommand.cpp */,
-                               372E12940F263D5A0095CF7E /* readdistcommand.h */,
-                               372E12950F263D5A0095CF7E /* readdistcommand.cpp */,
-                               372E126E0F26365B0095CF7E /* readotucommand.h */,
-                               372E126F0F26365B0095CF7E /* readotucommand.cpp */,
-                               37E5F4900F2A3DA800F8D827 /* readtreecommand.h */,
-                               37E5F4910F2A3DA800F8D827 /* readtreecommand.cpp */,
-                               37B73CBE1004EB38008C4B41 /* removeseqscommand.h */,
-                               37B73CBF1004EB38008C4B41 /* removeseqscommand.cpp */,
-                               7E09C5120FDA79C5002ECAE5 /* reversecommand.h */,
-                               7E09C5130FDA79C5002ECAE5 /* reversecommand.cpp */,
-                               A70DECD71063D8B40057C03C /* secondarystructurecommand.h */,
-                               A70DECD81063D8B40057C03C /* secondarystructurecommand.cpp */,
-                               371B30B30FD7EE67000414CA /* screenseqscommand.h */,
-                               371B30B20FD7EE67000414CA /* screenseqscommand.cpp */,
-                               3799A94F0FD6A58C00E33EDE /* seqsummarycommand.h */,
-                               3799A94E0FD6A58C00E33EDE /* seqsummarycommand.cpp */,
-                               A70B00C6110885EB002F453A /* setdircommand.h */,
-                               A70B00C7110885EB002F453A /* setdircommand.cpp */,
-                               37D928270F21331F001D4494 /* sharedcommand.h */,
-                               37D928260F21331F001D4494 /* sharedcommand.cpp */,
-                               37D928470F21331F001D4494 /* summarycommand.h */,
-                               37D928460F21331F001D4494 /* summarycommand.cpp */,
-                               37D9284B0F21331F001D4494 /* summarysharedcommand.h */,
-                               37D9284A0F21331F001D4494 /* summarysharedcommand.cpp */,
-                               37B73CCD1004F5E0008C4B41 /* systemcommand.h */,
-                               37B73CCE1004F5E0008C4B41 /* systemcommand.cpp */,
-                               211C38370F961E1F00FEE541 /* treegroupscommand.h */,
-                               211C38360F961E1F00FEE541 /* treegroupscommand.cpp */,
-                               7E09C5340FDA7F65002ECAE5 /* trimseqscommand.h */,
-                               7E09C5350FDA7F65002ECAE5 /* trimseqscommand.cpp */,
-                               3746109B0F40657600460C57 /* unifracunweightedcommand.h */,
-                               3746109C0F40657600460C57 /* unifracunweightedcommand.cpp */,
-                               374610760F40645300460C57 /* unifracweightedcommand.h */,
-                               374610770F40645300460C57 /* unifracweightedcommand.cpp */,
-                               37519A9F0F810D0200FED5E8 /* venncommand.h */,
-                               37519AA00F810D0200FED5E8 /* venncommand.cpp */,
+                               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 = commands;
+                       name = chimera;
                        sourceTree = "<group>";
                };
-               37D928AC0F213420001D4494 /* containers */ = {
+               A7E9BA4B12D3966900DA6239 /* classifier */ = {
                        isa = PBXGroup;
                        children = (
-                               373C68A10FC1C07D00137ACD /* alignment.hpp */,
-                               373C68A00FC1C07D00137ACD /* alignment.cpp */,
-                               373C68A30FC1C07D00137ACD /* alignmentcell.hpp */,
-                               373C68A20FC1C07D00137ACD /* alignmentcell.cpp */,
-                               A78782A910A1B1CB0086103D /* alignmentdb.h */,
-                               A78782AA10A1B1CB0086103D /* alignmentdb.cpp */,
-                               373C69170FC1C8AF00137ACD /* blastdb.hpp */,
-                               373C69160FC1C8AF00137ACD /* blastdb.cpp */,
-                               37D927D40F21331F001D4494 /* database.hpp */,
-                               37D927D30F21331F001D4494 /* database.cpp */,
-                               37D927D50F21331F001D4494 /* datavector.hpp */,
-                               A794201011107897003AECCD /* distancedb.hpp */,
-                               A794200F11107897003AECCD /* distancedb.cpp */,
-                               37D927DC0F21331F001D4494 /* fastamap.h */,
-                               37D927DB0F21331F001D4494 /* fastamap.cpp */,
-                               375873EA0F7D64520040F377 /* fullmatrix.h */,
-                               375873EB0F7D64520040F377 /* fullmatrix.cpp */,
-                               37D927E20F21331F001D4494 /* groupmap.h */,
-                               37D927E10F21331F001D4494 /* groupmap.cpp */,
-                               37D927EA0F21331F001D4494 /* kmer.hpp */,
-                               37D927E90F21331F001D4494 /* kmer.cpp */,
-                               37D927EC0F21331F001D4494 /* kmerdb.hpp */,
-                               37D927EB0F21331F001D4494 /* kmerdb.cpp */,
-                               37D927EE0F21331F001D4494 /* listvector.hpp */,
-                               37D927ED0F21331F001D4494 /* listvector.cpp */,
-                               37D927F10F21331F001D4494 /* nameassignment.hpp */,
-                               37D927F00F21331F001D4494 /* nameassignment.cpp */,
-                               37D927F80F21331F001D4494 /* ordervector.hpp */,
-                               37D927F70F21331F001D4494 /* ordervector.cpp */,
-                               37D928000F21331F001D4494 /* rabundvector.hpp */,
-                               37D927FF0F21331F001D4494 /* rabundvector.cpp */,
-                               37D9281B0F21331F001D4494 /* sabundvector.hpp */,
-                               37D9281A0F21331F001D4494 /* sabundvector.cpp */,
-                               37D9281D0F21331F001D4494 /* sequence.hpp */,
-                               37D9281C0F21331F001D4494 /* sequence.cpp */,
-                               378C1AFE0FB0644D004D63F5 /* sequencedb.h */,
-                               378C1AFD0FB0644D004D63F5 /* sequencedb.cpp */,
-                               37AD4CE20F28AEA300AA2D49 /* sharedlistvector.h */,
-                               37AD4CE30F28AEA300AA2D49 /* sharedlistvector.cpp */,
-                               37D9282F0F21331F001D4494 /* sharedordervector.h */,
-                               37D9282E0F21331F001D4494 /* sharedordervector.cpp */,
-                               37D928310F21331F001D4494 /* sharedrabundvector.h */,
-                               37D928300F21331F001D4494 /* sharedrabundvector.cpp */,
-                               37D928330F21331F001D4494 /* sharedsabundvector.h */,
-                               37D928320F21331F001D4494 /* sharedsabundvector.cpp */,
-                               37D928450F21331F001D4494 /* sparsematrix.hpp */,
-                               37D928440F21331F001D4494 /* sparsematrix.cpp */,
-                               373C68F40FC1C6A800137ACD /* suffixdb.hpp */,
-                               373C68F30FC1C6A800137ACD /* suffixdb.cpp */,
-                               373C68F60FC1C6A800137ACD /* suffixnodes.hpp */,
-                               373C68F50FC1C6A800137ACD /* suffixnodes.cpp */,
-                               373C68F80FC1C6A800137ACD /* suffixtree.hpp */,
-                               373C68F70FC1C6A800137ACD /* suffixtree.cpp */,
-                               37AD4DB90F28E2FE00AA2D49 /* tree.h */,
-                               37AD4DBA0F28E2FE00AA2D49 /* tree.cpp */,
-                               379293C10F2DE73400B9034A /* treemap.h */,
-                               379293C20F2DE73400B9034A /* treemap.cpp */,
-                               37E5F3E10F29FD4200F8D827 /* treenode.h */,
-                               37E5F3E20F29FD4200F8D827 /* treenode.cpp */,
+                               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 = containers;
+                       name = classifier;
+                       sourceTree = "<group>";
+               };
+               A7E9BA4F12D398D700DA6239 /* clearcut */ = {
+                       isa = PBXGroup;
+                       children = (
+                               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 = clearcut;
                        sourceTree = "<group>";
                };
-               37D928B10F213472001D4494 /* errorcheckor */ = {
+               A7E9BA5312D39A5E00DA6239 /* read */ = {
                        isa = PBXGroup;
                        children = (
-                               37D928500F21331F001D4494 /* validcalculator.h */,
-                               37D9284F0F21331F001D4494 /* validcalculator.cpp */,
-                               37D928540F21331F001D4494 /* validparameter.h */,
-                               37D928530F21331F001D4494 /* validparameter.cpp */,
+                               A7E9B6E912D37EC400DA6239 /* formatcolumn.cpp */,
+                               A7E9B6EA12D37EC400DA6239 /* formatcolumn.h */,
+                               A7E9B6EB12D37EC400DA6239 /* formatmatrix.h */,
+                               A7E9B6EC12D37EC400DA6239 /* formatphylip.cpp */,
+                               A7E9B6ED12D37EC400DA6239 /* formatphylip.h */,
+                               A7E9B7B012D37EC400DA6239 /* readblast.cpp */,
+                               A7E9B7B112D37EC400DA6239 /* readblast.h */,
+                               A7E9B7B212D37EC400DA6239 /* readcluster.cpp */,
+                               A7E9B7B312D37EC400DA6239 /* readcluster.h */,
+                               A7E9B7B412D37EC400DA6239 /* readcolumn.cpp */,
+                               A7E9B7B512D37EC400DA6239 /* readcolumn.h */,
+                               A7E9B7B812D37EC400DA6239 /* readmatrix.hpp */,
+                               A7E9B7B912D37EC400DA6239 /* readotu.cpp */,
+                               A7E9B7BA12D37EC400DA6239 /* readotu.h */,
+                               A7E9B7BD12D37EC400DA6239 /* readphylip.cpp */,
+                               A7E9B7BE12D37EC400DA6239 /* readphylip.h */,
+                               A7E9B7BF12D37EC400DA6239 /* readtree.cpp */,
+                               A7E9B7C012D37EC400DA6239 /* readtree.h */,
+                               A713EBAA12DC7613000092AC /* readphylipvector.h */,
+                               A713EBAB12DC7613000092AC /* readphylipvector.cpp */,
+                               A7E9B84312D37EC400DA6239 /* splitmatrix.cpp */,
+                               A7E9B84412D37EC400DA6239 /* splitmatrix.h */,
                        );
-                       name = errorcheckor;
+                       name = read;
                        sourceTree = "<group>";
                };
-               A787811210A073F40086103D /* classifiers */ = {
+               A7E9BA5612D39BD800DA6239 /* metastats */ = {
                        isa = PBXGroup;
                        children = (
-                               A78780FE10A06B8B0086103D /* classify.h */,
-                               A787810210A06D5D0086103D /* classify.cpp */,
-                               A787820F10A0AAE70086103D /* bayesian.h */,
-                               A787821010A0AAE70086103D /* bayesian.cpp */,
-                               A773805D10B6D6FC002A6A61 /* taxonomyequalizer.h */,
-                               A773805E10B6D6FC002A6A61 /* taxonomyequalizer.cpp */,
-                               A78781B910A0813D0086103D /* phylotree.h */,
-                               A78781B810A0813D0086103D /* phylotree.cpp */,
-                               A787844310A1EBDD0086103D /* knn.h */,
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                                GCC_WARN_UNUSED_VARIABLE = YES;
+                               INSTALL_PATH = "";
+                               MACH_O_TYPE = mh_execute;
                                OTHER_CPLUSPLUSFLAGS = (
-                                       "-ansi",
-                                       "-pedantic",
-                                       "-wall",
-                                       "-lreadline",
                                        "-DUSE_READLINE",
+                                       "-DBIT_VERSION",
+                                       "$(OTHER_CFLAGS)",
+                               );
+                               OTHER_LDFLAGS = (
+                                       "-lncurses",
+                                       "-lreadline",
                                );
                                PREBINDING = NO;
-                               SDKROOT = "$(DEVELOPER_SDK_DIR)/MacOSX10.5.sdk";
-                               SYMROOT = /Users/johnwestcott/Desktop;
-                               WARNING_CFLAGS = "";
+                               SDKROOT = macosx10.5;
                        };
                        name = Release;
                };
 /* End XCBuildConfiguration section */
 
 /* Begin XCConfigurationList section */
-               1DEB923108733DC60010E9CD /* Build configuration list for PBXNativeTarget "mothur" */ = {
+               1DEB928508733DD80010E9CD /* Build configuration list for PBXNativeTarget "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
-                               1DEB923208733DC60010E9CD /* Debug */,
-                               1DEB923308733DC60010E9CD /* Release */,
+                               1DEB928608733DD80010E9CD /* Debug */,
+                               1DEB928708733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;
                };
-               1DEB923508733DC60010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
+               1DEB928908733DD80010E9CD /* Build configuration list for PBXProject "Mothur" */ = {
                        isa = XCConfigurationList;
                        buildConfigurations = (
-                               1DEB923608733DC60010E9CD /* Debug */,
-                               1DEB923708733DC60010E9CD /* Release */,
+                               1DEB928A08733DD80010E9CD /* Debug */,
+                               1DEB928B08733DD80010E9CD /* Release */,
                        );
                        defaultConfigurationIsVisible = 0;
                        defaultConfigurationName = Release;