From 0caf3fbabaa3ece404f8ce77f4c883dc5b1bf1dc Mon Sep 17 00:00:00 2001
From: Sarah Westcott <mothur.westcott@gmail.com>
Date: Wed, 2 May 2012 12:03:00 -0400
Subject: [PATCH] Revert to previous commit

---
 Mothur.xcodeproj/project.pbxproj              | 1300 ++++++++---------
 source/ace.cpp => ace.cpp                     |    0
 source/ace.h => ace.h                         |    0
 source/aligncommand.cpp => aligncommand.cpp   |    0
 source/aligncommand.h => aligncommand.h       |    2 +-
 source/alignment.cpp => alignment.cpp         |    0
 source/alignment.hpp => alignment.hpp         |    0
 source/alignmentcell.cpp => alignmentcell.cpp |    0
 source/alignmentcell.hpp => alignmentcell.hpp |    0
 source/alignmentdb.cpp => alignmentdb.cpp     |    0
 source/alignmentdb.h => alignmentdb.h         |    0
 source/amovacommand.cpp => amovacommand.cpp   |    0
 source/amovacommand.h => amovacommand.h       |    0
 source/anosimcommand.cpp => anosimcommand.cpp |    0
 source/anosimcommand.h => anosimcommand.h     |    0
 .../averagelinkage.cpp => averagelinkage.cpp  |    0
 source/bayesian.cpp => bayesian.cpp           |    0
 source/bayesian.h => bayesian.h               |    0
 source/bellerophon.cpp => bellerophon.cpp     |    0
 source/bellerophon.h => bellerophon.h         |    0
 source/bergerparker.cpp => bergerparker.cpp   |    0
 source/bergerparker.h => bergerparker.h       |    0
 ...uencecommand.cpp => binsequencecommand.cpp |    0
 ...nsequencecommand.h => binsequencecommand.h |    0
 source/blastalign.cpp => blastalign.cpp       |    0
 source/blastalign.hpp => blastalign.hpp       |    0
 source/blastdb.cpp => blastdb.cpp             |    0
 source/blastdb.hpp => blastdb.hpp             |    0
 source/boneh.cpp => boneh.cpp                 |    0
 source/boneh.h => boneh.h                     |    0
 source/bootstrap.cpp => bootstrap.cpp         |    0
 source/bootstrap.h => bootstrap.h             |    0
 source/bsplvb.f => bsplvb.f                   |    0
 source/bsplvd.f => bsplvd.f                   |    0
 source/bstick.cpp => bstick.cpp               |    0
 source/bstick.h => bstick.h                   |    0
 source/bvalue.f => bvalue.f                   |    0
 source/calculator.cpp => calculator.cpp       |    0
 source/calculator.h => calculator.h           |    0
 source/canberra.cpp => canberra.cpp           |    0
 source/canberra.h => canberra.h               |    0
 ...catchallcommand.cpp => catchallcommand.cpp |    0
 source/catchallcommand.h => catchallcommand.h |    0
 source/ccode.cpp => ccode.cpp                 |    0
 source/ccode.h => ccode.h                     |    0
 source/chao1.cpp => chao1.cpp                 |    0
 source/chao1.h => chao1.h                     |    0
 source/chimera.cpp => chimera.cpp             |    0
 source/chimera.h => chimera.h                 |    0
 ...mmand.cpp => chimerabellerophoncommand.cpp |    0
 ...oncommand.h => chimerabellerophoncommand.h |    0
 ...codecommand.cpp => chimeraccodecommand.cpp |    0
 ...eraccodecommand.h => chimeraccodecommand.h |    0
 ...heckcommand.cpp => chimeracheckcommand.cpp |    0
 ...eracheckcommand.h => chimeracheckcommand.h |    0
 ...chimeracheckrdp.cpp => chimeracheckrdp.cpp |    0
 source/chimeracheckrdp.h => chimeracheckrdp.h |    0
 ...uscommand.cpp => chimeraperseuscommand.cpp |    0
 ...erseuscommand.h => chimeraperseuscommand.h |    0
 ...ilcommand.cpp => chimerapintailcommand.cpp |    0
 ...intailcommand.h => chimerapintailcommand.h |    0
 ...imerarealigner.cpp => chimerarealigner.cpp |    0
 .../chimerarealigner.h => chimerarealigner.h  |    0
 source/chimeraslayer.cpp => chimeraslayer.cpp |    0
 source/chimeraslayer.h => chimeraslayer.h     |    0
 ...yercommand.cpp => chimeraslayercommand.cpp |    0
 ...aslayercommand.h => chimeraslayercommand.h |    0
 ...imecommand.cpp => chimerauchimecommand.cpp |    0
 ...auchimecommand.h => chimerauchimecommand.h |    0
 ...chopseqscommand.cpp => chopseqscommand.cpp |    0
 source/chopseqscommand.h => chopseqscommand.h |    0
 source/classify.cpp => classify.cpp           |    0
 source/classify.h => classify.h               |    0
 ...fyotucommand.cpp => classifyotucommand.cpp |    0
 ...assifyotucommand.h => classifyotucommand.h |    0
 ...seqscommand.cpp => classifyseqscommand.cpp |    0
 ...sifyseqscommand.h => classifyseqscommand.h |    0
 ...treecommand.cpp => classifytreecommand.cpp |    0
 ...sifytreecommand.h => classifytreecommand.h |    0
 source/clearcut.cpp => clearcut.cpp           |    0
 source/clearcut.h => clearcut.h               |    0
 ...clearcutcommand.cpp => clearcutcommand.cpp |    0
 source/clearcutcommand.h => clearcutcommand.h |    0
 ...emorycommand.cpp => clearmemorycommand.cpp |    0
 ...earmemorycommand.h => clearmemorycommand.h |    0
 source/cluster.cpp => cluster.cpp             |    0
 source/cluster.hpp => cluster.hpp             |    0
 .../clusterclassic.cpp => clusterclassic.cpp  |    0
 source/clusterclassic.h => clusterclassic.h   |    0
 .../clustercommand.cpp => clustercommand.cpp  |    0
 source/clustercommand.h => clustercommand.h   |    0
 ...oturcommand.cpp => clusterdoturcommand.cpp |    0
 ...terdoturcommand.h => clusterdoturcommand.h |    0
 ...command.cpp => clusterfragmentscommand.cpp |    0
 ...entscommand.h => clusterfragmentscommand.h |    0
 ...plitcommand.cpp => clustersplitcommand.cpp |    0
 ...tersplitcommand.h => clustersplitcommand.h |    0
 source/cmdargs.cpp => cmdargs.cpp             |    0
 source/cmdargs.h => cmdargs.h                 |    0
 source/collect.cpp => collect.cpp             |    0
 source/collect.h => collect.h                 |    0
 .../collectcommand.cpp => collectcommand.cpp  |    0
 source/collectcommand.h => collectcommand.h   |    0
 source/collectdisplay.h => collectdisplay.h   |    0
 ...ectorscurvedata.h => collectorscurvedata.h |    0
 ...redcommand.cpp => collectsharedcommand.cpp |    0
 ...tsharedcommand.h => collectsharedcommand.h |    0
 source/command.hpp => command.hpp             |    0
 .../commandfactory.cpp => commandfactory.cpp  |    0
 .../commandfactory.hpp => commandfactory.hpp  |    0
 ...ptionparser.cpp => commandoptionparser.cpp |    0
 ...ptionparser.hpp => commandoptionparser.hpp |    0
 .../commandparameter.h => commandparameter.h  |    0
 source/common.h => common.h                   |    0
 ...completelinkage.cpp => completelinkage.cpp |    0
 source/consensus.cpp => consensus.cpp         |    0
 source/consensus.h => consensus.h             |    0
 ...eqscommand.cpp => consensusseqscommand.cpp |    0
 ...susseqscommand.h => consensusseqscommand.h |    0
 ...encecommand.cpp => cooccurrencecommand.cpp |    0
 ...currencecommand.h => cooccurrencecommand.h |    0
 ...corraxescommand.cpp => corraxescommand.cpp |    0
 source/corraxescommand.h => corraxescommand.h |    0
 ...roupscommand.cpp => countgroupscommand.cpp |    0
 ...untgroupscommand.h => countgroupscommand.h |    0
 ...untseqscommand.cpp => countseqscommand.cpp |    0
 .../countseqscommand.h => countseqscommand.h  |    0
 source/coverage.cpp => coverage.cpp           |    0
 source/coverage.h => coverage.h               |    0
 ...secommand.cpp => createdatabasecommand.cpp |    0
 ...tabasecommand.h => createdatabasecommand.h |    0
 source/currentfile.h => currentfile.h         |    0
 source/database.cpp => database.cpp           |    0
 source/database.hpp => database.hpp           |    0
 source/datavector.hpp => datavector.hpp       |    0
 source/daxpy.f => daxpy.f                     |    0
 source/dayhoff.h => dayhoff.h                 |    0
 source/ddot.f => ddot.f                       |    0
 source/decalc.cpp => decalc.cpp               |    0
 source/decalc.h => decalc.h                   |    0
 ...olutecommand.cpp => deconvolutecommand.cpp |    0
 ...convolutecommand.h => deconvolutecommand.h |    0
 ...gapseqscommand.cpp => degapseqscommand.cpp |    0
 .../degapseqscommand.h => degapseqscommand.h  |    0
 ...seqscommand.cpp => deuniqueseqscommand.cpp |    0
 ...iqueseqscommand.h => deuniqueseqscommand.h |    0
 ...treecommand.cpp => deuniquetreecommand.cpp |    0
 ...iquetreecommand.h => deuniquetreecommand.h |    0
 source/display.h => display.h                 |    0
 source/dist.h => dist.h                       |    0
 ...distancecommand.cpp => distancecommand.cpp |    0
 source/distancecommand.h => distancecommand.h |    0
 source/distancedb.cpp => distancedb.cpp       |    0
 source/distancedb.hpp => distancedb.hpp       |    0
 source/distclearcut.cpp => distclearcut.cpp   |    0
 source/distclearcut.h => distclearcut.h       |    0
 source/dlibshuff.cpp => dlibshuff.cpp         |    0
 source/dlibshuff.h => dlibshuff.h             |    0
 source/dmat.cpp => dmat.cpp                   |    0
 source/dmat.h => dmat.h                       |    0
 source/dpbfa.f => dpbfa.f                     |    0
 source/dpbsl.f => dpbsl.f                     |    0
 source/eachgapdist.h => eachgapdist.h         |    0
 ...gapdistignorens.h => eachgapdistignorens.h |    0
 source/eachgapignore.h => eachgapignore.h     |    0
 source/efron.cpp => efron.cpp                 |    0
 source/efron.h => efron.h                     |    0
 .../endiannessmacros.h => endiannessmacros.h  |    0
 source/engine.cpp => engine.cpp               |    0
 source/engine.hpp => engine.hpp               |    0
 source/fasta.cpp => fasta.cpp                 |    0
 source/fasta.h => fasta.h                     |    0
 source/fastamap.cpp => fastamap.cpp           |    0
 source/fastamap.h => fastamap.h               |    0
 source/fileoutput.cpp => fileoutput.cpp       |    0
 source/fileoutput.h => fileoutput.h           |    0
 source/filters.h => filters.h                 |    0
 ...erseqscommand.cpp => filterseqscommand.cpp |    0
 ...filterseqscommand.h => filterseqscommand.h |    0
 source/flowdata.cpp => flowdata.cpp           |    0
 source/flowdata.h => flowdata.h               |    0
 source/formatcolumn.cpp => formatcolumn.cpp   |    0
 source/formatcolumn.h => formatcolumn.h       |    0
 source/formatmatrix.h => formatmatrix.h       |    0
 source/formatphylip.cpp => formatphylip.cpp   |    0
 source/formatphylip.h => formatphylip.h       |    0
 source/fullmatrix.cpp => fullmatrix.cpp       |    0
 source/fullmatrix.h => fullmatrix.h           |    0
 source/geom.cpp => geom.cpp                   |    0
 source/geom.h => geom.h                       |    0
 ...focommand.cpp => getcommandinfocommand.cpp |    0
 ...ndinfocommand.h => getcommandinfocommand.h |    0
 ...urrentcommand.cpp => getcurrentcommand.cpp |    0
 ...getcurrentcommand.h => getcurrentcommand.h |    0
 ...getgroupcommand.cpp => getgroupcommand.cpp |    0
 source/getgroupcommand.h => getgroupcommand.h |    0
 ...tgroupscommand.cpp => getgroupscommand.cpp |    0
 .../getgroupscommand.h => getgroupscommand.h  |    0
 ...getlabelcommand.cpp => getlabelcommand.cpp |    0
 source/getlabelcommand.h => getlabelcommand.h |    0
 ...ineagecommand.cpp => getlineagecommand.cpp |    0
 ...getlineagecommand.h => getlineagecommand.h |    0
 ...ountcommand.cpp => getlistcountcommand.cpp |    0
 ...istcountcommand.h => getlistcountcommand.h |    0
 source/getopt_long.cpp => getopt_long.cpp     |    0
 source/getopt_long.h => getopt_long.h         |    0
 ...toturepcommand.cpp => getoturepcommand.cpp |    0
 .../getoturepcommand.h => getoturepcommand.h  |    0
 .../getotuscommand.cpp => getotuscommand.cpp  |    0
 source/getotuscommand.h => getotuscommand.h   |    0
 ...trabundcommand.cpp => getrabundcommand.cpp |    0
 .../getrabundcommand.h => getrabundcommand.h  |    0
 ...abundcommand.cpp => getrelabundcommand.cpp |    0
 ...trelabundcommand.h => getrelabundcommand.h |    0
 ...tsabundcommand.cpp => getsabundcommand.cpp |    0
 .../getsabundcommand.h => getsabundcommand.h  |    0
 .../getseqscommand.cpp => getseqscommand.cpp  |    0
 source/getseqscommand.h => getseqscommand.h   |    0
 ...dotucommand.cpp => getsharedotucommand.cpp |    0
 ...haredotucommand.h => getsharedotucommand.h |    0
 source/goodscoverage.cpp => goodscoverage.cpp |    0
 source/goodscoverage.h => goodscoverage.h     |    0
 source/gotohoverlap.cpp => gotohoverlap.cpp   |    0
 source/gotohoverlap.hpp => gotohoverlap.hpp   |    0
 source/gower.cpp => gower.cpp                 |    0
 source/gower.h => gower.h                     |    0
 source/groupmap.cpp => groupmap.cpp           |    0
 source/groupmap.h => groupmap.h               |    0
 source/hamming.cpp => hamming.cpp             |    0
 source/hamming.h => hamming.h                 |    0
 source/hcluster.cpp => hcluster.cpp           |    0
 source/hcluster.h => hcluster.h               |    0
 ...hclustercommand.cpp => hclustercommand.cpp |    0
 source/hclustercommand.h => hclustercommand.h |    0
 source/heatmap.cpp => heatmap.cpp             |    0
 source/heatmap.h => heatmap.h                 |    0
 .../heatmapcommand.cpp => heatmapcommand.cpp  |    0
 source/heatmapcommand.h => heatmapcommand.h   |    0
 source/heatmapsim.cpp => heatmapsim.cpp       |    0
 source/heatmapsim.h => heatmapsim.h           |    0
 ...mapsimcommand.cpp => heatmapsimcommand.cpp |    0
 ...heatmapsimcommand.h => heatmapsimcommand.h |    0
 source/heip.cpp => heip.cpp                   |    0
 source/heip.h => heip.h                       |    0
 source/hellinger.cpp => hellinger.cpp         |    0
 source/hellinger.h => hellinger.h             |    0
 source/helpcommand.cpp => helpcommand.cpp     |    0
 source/helpcommand.h => helpcommand.h         |    0
 source/homovacommand.cpp => homovacommand.cpp |    0
 source/homovacommand.h => homovacommand.h     |    0
 source/ignoregaps.h => ignoregaps.h           |    0
 ...dicatorcommand.cpp => indicatorcommand.cpp |    0
 .../indicatorcommand.h => indicatorcommand.h  |    0
 source/inputdata.cpp => inputdata.cpp         |    0
 source/inputdata.h => inputdata.h             |    0
 source/interv.f => interv.f                   |    0
 source/intrv.f => intrv.f                     |    0
 source/invsimpson.cpp => invsimpson.cpp       |    0
 source/invsimpson.h => invsimpson.h           |    0
 source/jackknife.cpp => jackknife.cpp         |    0
 source/jackknife.h => jackknife.h             |    0
 source/kmer.cpp => kmer.cpp                   |    0
 source/kmer.hpp => kmer.hpp                   |    0
 source/kmerdb.cpp => kmerdb.cpp               |    0
 source/kmerdb.hpp => kmerdb.hpp               |    0
 source/knn.cpp => knn.cpp                     |    0
 source/knn.h => knn.h                         |    0
 source/libshuff.cpp => libshuff.cpp           |    0
 source/libshuff.h => libshuff.h               |    0
 ...libshuffcommand.cpp => libshuffcommand.cpp |    0
 source/libshuffcommand.h => libshuffcommand.h |    0
 source/linearalgebra.cpp => linearalgebra.cpp |    0
 source/linearalgebra.h => linearalgebra.h     |    0
 ...listseqscommand.cpp => listseqscommand.cpp |    0
 source/listseqscommand.h => listseqscommand.h |    0
 source/listvector.cpp => listvector.cpp       |    0
 source/listvector.hpp => listvector.hpp       |    0
 source/logsd.cpp => logsd.cpp                 |    0
 source/logsd.h => logsd.h                     |    0
 ...makebiomcommand.cpp => makebiomcommand.cpp |    0
 source/makebiomcommand.h => makebiomcommand.h |    0
 ...kefastqcommand.cpp => makefastqcommand.cpp |    0
 .../makefastqcommand.h => makefastqcommand.h  |    0
 source/makefile => makefile                   |    0
 ...kegroupcommand.cpp => makegroupcommand.cpp |    0
 .../makegroupcommand.h => makegroupcommand.h  |    0
 source/maligner.cpp => maligner.cpp           |    0
 source/maligner.h => maligner.h               |    0
 source/manhattan.cpp => manhattan.cpp         |    0
 source/manhattan.h => manhattan.h             |    0
 source/mantelcommand.cpp => mantelcommand.cpp |    0
 source/mantelcommand.h => mantelcommand.h     |    0
 ...tputcommand.cpp => matrixoutputcommand.cpp |    0
 ...ixoutputcommand.h => matrixoutputcommand.h |    0
 source/memchi2.cpp => memchi2.cpp             |    0
 source/memchi2.h => memchi2.h                 |    0
 source/memchord.cpp => memchord.cpp           |    0
 source/memchord.h => memchord.h               |    0
 source/memeuclidean.cpp => memeuclidean.cpp   |    0
 source/memeuclidean.h => memeuclidean.h       |    0
 source/mempearson.cpp => mempearson.cpp       |    0
 source/mempearson.h => mempearson.h           |    0
 ...rgefilecommand.cpp => mergefilecommand.cpp |    0
 .../mergefilecommand.h => mergefilecommand.h  |    0
 ...roupscommand.cpp => mergegroupscommand.cpp |    0
 ...rgegroupscommand.h => mergegroupscommand.h |    0
 ...tastatscommand.cpp => metastatscommand.cpp |    0
 .../metastatscommand.h => metastatscommand.h  |    0
 ...clustercommand.cpp => mgclustercommand.cpp |    0
 .../mgclustercommand.h => mgclustercommand.h  |    0
 source/mothur.cpp => mothur.cpp               |    0
 source/mothur.h => mothur.h                   |    0
 source/mothurfisher.cpp => mothurfisher.cpp   |    0
 source/mothurfisher.h => mothurfisher.h       |    0
 ...mothurmetastats.cpp => mothurmetastats.cpp |    0
 source/mothurmetastats.h => mothurmetastats.h |    0
 source/mothurout.cpp => mothurout.cpp         |    0
 source/mothurout.h => mothurout.h             |    0
 source/myPerseus.cpp => myPerseus.cpp         |    0
 source/myPerseus.h => myPerseus.h             |    0
 source/myseqdist.cpp => myseqdist.cpp         |    0
 source/myseqdist.h => myseqdist.h             |    0
 .../nameassignment.cpp => nameassignment.cpp  |    0
 .../nameassignment.hpp => nameassignment.hpp  |    0
 source/nast.cpp => nast.cpp                   |    0
 source/nast.hpp => nast.hpp                   |    0
 source/nastreport.cpp => nastreport.cpp       |    0
 source/nastreport.hpp => nastreport.hpp       |    0
 ...edlemanoverlap.cpp => needlemanoverlap.cpp |    0
 ...edlemanoverlap.hpp => needlemanoverlap.hpp |    0
 source/nmdscommand.cpp => nmdscommand.cpp     |    0
 source/nmdscommand.h => nmdscommand.h         |    0
 source/noalign.cpp => noalign.cpp             |    0
 source/noalign.hpp => noalign.hpp             |    0
 source/nocommands.cpp => nocommands.cpp       |    0
 source/nocommands.h => nocommands.h           |    0
 ...dcommand.cpp => normalizesharedcommand.cpp |    0
 ...haredcommand.h => normalizesharedcommand.h |    0
 source/npshannon.cpp => npshannon.cpp         |    0
 source/npshannon.h => npshannon.h             |    0
 source/nseqs.h => nseqs.h                     |    0
 source/observable.h => observable.h           |    0
 source/odum.cpp => odum.cpp                   |    0
 source/odum.h => odum.h                       |    0
 source/onegapdist.h => onegapdist.h           |    0
 source/onegapignore.h => onegapignore.h       |    0
 source/optionparser.cpp => optionparser.cpp   |    0
 source/optionparser.h => optionparser.h       |    0
 source/ordervector.cpp => ordervector.cpp     |    0
 source/ordervector.hpp => ordervector.hpp     |    0
 ...oncommand.cpp => otuassociationcommand.cpp |    0
 ...iationcommand.h => otuassociationcommand.h |    0
 ...rchycommand.cpp => otuhierarchycommand.cpp |    0
 ...ierarchycommand.h => otuhierarchycommand.h |    0
 source/overlap.cpp => overlap.cpp             |    0
 source/overlap.hpp => overlap.hpp             |    0
 ...seqscommand.cpp => pairwiseseqscommand.cpp |    0
 ...wiseseqscommand.h => pairwiseseqscommand.h |    0
 ...astaqcommand.cpp => parsefastaqcommand.cpp |    0
 ...rsefastaqcommand.h => parsefastaqcommand.h |    0
 ...elistscommand.cpp => parselistscommand.cpp |    0
 ...parselistscommand.h => parselistscommand.h |    0
 source/parsimony.cpp => parsimony.cpp         |    0
 source/parsimony.h => parsimony.h             |    0
 ...rsimonycommand.cpp => parsimonycommand.cpp |    0
 .../parsimonycommand.h => parsimonycommand.h  |    0
 source/pcacommand.cpp => pcacommand.cpp       |    0
 source/pcacommand.h => pcacommand.h           |    0
 source/pcoacommand.cpp => pcoacommand.cpp     |    0
 source/pcoacommand.h => pcoacommand.h         |    0
 source/pcrseqscommand.h => pcrseqscommand.h   |    0
 ...tycommand.cpp => phylodiversitycommand.cpp |    0
 ...ersitycommand.h => phylodiversitycommand.h |    0
 source/phylosummary.cpp => phylosummary.cpp   |    0
 source/phylosummary.h => phylosummary.h       |    0
 source/phylotree.cpp => phylotree.cpp         |    0
 source/phylotree.h => phylotree.h             |    0
 ...ylotypecommand.cpp => phylotypecommand.cpp |    0
 .../phylotypecommand.h => phylotypecommand.h  |    0
 source/pintail.cpp => pintail.cpp             |    0
 source/pintail.h => pintail.h                 |    0
 ...nepdscommand.cpp => pipelinepdscommand.cpp |    0
 ...pelinepdscommand.h => pipelinepdscommand.h |    0
 .../prcseqscommand.cpp => prcseqscommand.cpp  |    0
 ...lustercommand.cpp => preclustercommand.cpp |    0
 ...preclustercommand.h => preclustercommand.h |    0
 source/prng.cpp => prng.cpp                   |    0
 source/prng.h => prng.h                       |    0
 source/progress.cpp => progress.cpp           |    0
 source/progress.hpp => progress.hpp           |    0
 source/qstat.cpp => qstat.cpp                 |    0
 source/qstat.h => qstat.h                     |    0
 source/qualityscores.cpp => qualityscores.cpp |    0
 source/qualityscores.h => qualityscores.h     |    0
 source/quitcommand.cpp => quitcommand.cpp     |    0
 source/quitcommand.h => quitcommand.h         |    0
 source/rabundvector.cpp => rabundvector.cpp   |    0
 source/rabundvector.hpp => rabundvector.hpp   |    0
 source/rarecalc.cpp => rarecalc.cpp           |    0
 source/rarecalc.h => rarecalc.h               |    0
 source/raredisplay.cpp => raredisplay.cpp     |    0
 source/raredisplay.h => raredisplay.h         |    0
 source/rarefact.cpp => rarefact.cpp           |    0
 source/rarefact.h => rarefact.h               |    0
 ...rarefactcommand.cpp => rarefactcommand.cpp |    0
 source/rarefactcommand.h => rarefactcommand.h |    0
 ...ctioncurvedata.h => rarefactioncurvedata.h |    0
 ...edcommand.cpp => rarefactsharedcommand.cpp |    0
 ...sharedcommand.h => rarefactsharedcommand.h |    0
 source/readblast.cpp => readblast.cpp         |    0
 source/readblast.h => readblast.h             |    0
 source/readcluster.cpp => readcluster.cpp     |    0
 source/readcluster.h => readcluster.h         |    0
 source/readcolumn.cpp => readcolumn.cpp       |    0
 source/readcolumn.h => readcolumn.h           |    0
 ...readdistcommand.cpp => readdistcommand.cpp |    0
 source/readdistcommand.h => readdistcommand.h |    0
 source/readmatrix.hpp => readmatrix.hpp       |    0
 .../readotucommand.cpp => readotucommand.cpp  |    0
 source/readotucommand.h => readotucommand.h   |    0
 source/readphylip.cpp => readphylip.cpp       |    0
 source/readphylip.h => readphylip.h           |    0
 ...adphylipvector.cpp => readphylipvector.cpp |    0
 .../readphylipvector.h => readphylipvector.h  |    0
 source/readtree.cpp => readtree.cpp           |    0
 source/readtree.h => readtree.h               |    0
 ...readtreecommand.cpp => readtreecommand.cpp |    0
 source/readtreecommand.h => readtreecommand.h |    0
 .../refchimeratest.cpp => refchimeratest.cpp  |    0
 source/refchimeratest.h => refchimeratest.h   |    0
 source/referencedb.cpp => referencedb.cpp     |    0
 source/referencedb.h => referencedb.h         |    0
 ...oupscommand.cpp => removegroupscommand.cpp |    0
 ...vegroupscommand.h => removegroupscommand.h |    0
 ...agecommand.cpp => removelineagecommand.cpp |    0
 ...lineagecommand.h => removelineagecommand.h |    0
 ...veotuscommand.cpp => removeotuscommand.cpp |    0
 ...removeotuscommand.h => removeotuscommand.h |    0
 ...verarecommand.cpp => removerarecommand.cpp |    0
 ...removerarecommand.h => removerarecommand.h |    0
 ...veseqscommand.cpp => removeseqscommand.cpp |    0
 ...removeseqscommand.h => removeseqscommand.h |    0
 source/reportfile.cpp => reportfile.cpp       |    0
 source/reportfile.h => reportfile.h           |    0
 .../reversecommand.cpp => reversecommand.cpp  |    0
 source/reversecommand.h => reversecommand.h   |    0
 source/sabundvector.cpp => sabundvector.cpp   |    0
 source/sabundvector.hpp => sabundvector.hpp   |    0
 ...enseqscommand.cpp => screenseqscommand.cpp |    0
 ...screenseqscommand.h => screenseqscommand.h |    0
 ...mmand.cpp => secondarystructurecommand.cpp |    0
 ...recommand.h => secondarystructurecommand.h |    0
 ...sensspeccommand.cpp => sensspeccommand.cpp |    0
 source/sensspeccommand.h => sensspeccommand.h |    0
 ...seqerrorcommand.cpp => seqerrorcommand.cpp |    0
 source/seqerrorcommand.h => seqerrorcommand.h |    0
 source/seqnoise.cpp => seqnoise.cpp           |    0
 source/seqnoise.h => seqnoise.h               |    0
 ...ummarycommand.cpp => seqsummarycommand.cpp |    0
 ...seqsummarycommand.h => seqsummarycommand.h |    0
 source/sequence.cpp => sequence.cpp           |    0
 source/sequence.hpp => sequence.hpp           |    0
 source/sequencedb.cpp => sequencedb.cpp       |    0
 source/sequencedb.h => sequencedb.h           |    0
 .../sequenceparser.cpp => sequenceparser.cpp  |    0
 source/sequenceparser.h => sequenceparser.h   |    0
 ...urrentcommand.cpp => setcurrentcommand.cpp |    0
 ...setcurrentcommand.h => setcurrentcommand.h |    0
 source/setdircommand.cpp => setdircommand.cpp |    0
 source/setdircommand.h => setdircommand.h     |    0
 ...ogfilecommand.cpp => setlogfilecommand.cpp |    0
 ...setlogfilecommand.h => setlogfilecommand.h |    0
 .../sffinfocommand.cpp => sffinfocommand.cpp  |    0
 source/sffinfocommand.h => sffinfocommand.h   |    0
 source/sgram.f => sgram.f                     |    0
 source/shannon.cpp => shannon.cpp             |    0
 source/shannon.h => shannon.h                 |    0
 source/shannoneven.cpp => shannoneven.cpp     |    0
 source/shannoneven.h => shannoneven.h         |    0
 source/sharedace.cpp => sharedace.cpp         |    0
 source/sharedace.h => sharedace.h             |    0
 ...aredanderbergs.cpp => sharedanderbergs.cpp |    0
 .../sharedanderbergs.h => sharedanderbergs.h  |    0
 ...aredbraycurtis.cpp => sharedbraycurtis.cpp |    0
 .../sharedbraycurtis.h => sharedbraycurtis.h  |    0
 source/sharedchao1.cpp => sharedchao1.cpp     |    0
 source/sharedchao1.h => sharedchao1.h         |    0
 source/sharedcommand.cpp => sharedcommand.cpp |    0
 source/sharedcommand.h => sharedcommand.h     |    0
 source/sharedjabund.cpp => sharedjabund.cpp   |    0
 source/sharedjabund.h => sharedjabund.h       |    0
 ...sharedjackknife.cpp => sharedjackknife.cpp |    0
 source/sharedjackknife.h => sharedjackknife.h |    0
 source/sharedjclass.cpp => sharedjclass.cpp   |    0
 source/sharedjclass.h => sharedjclass.h       |    0
 source/sharedjest.cpp => sharedjest.cpp       |    0
 source/sharedjest.h => sharedjest.h           |    0
 source/sharedkstest.cpp => sharedkstest.cpp   |    0
 source/sharedkstest.h => sharedkstest.h       |    0
 ...aredkulczynski.cpp => sharedkulczynski.cpp |    0
 .../sharedkulczynski.h => sharedkulczynski.h  |    0
 ...zynskicody.cpp => sharedkulczynskicody.cpp |    0
 ...kulczynskicody.h => sharedkulczynskicody.h |    0
 source/sharedlennon.cpp => sharedlennon.cpp   |    0
 source/sharedlennon.h => sharedlennon.h       |    0
 ...aredlistvector.cpp => sharedlistvector.cpp |    0
 .../sharedlistvector.h => sharedlistvector.h  |    0
 ...aredmarczewski.cpp => sharedmarczewski.cpp |    0
 .../sharedmarczewski.h => sharedmarczewski.h  |    0
 ...morisitahorn.cpp => sharedmorisitahorn.cpp |    0
 ...aredmorisitahorn.h => sharedmorisitahorn.h |    0
 source/sharednseqs.h => sharednseqs.h         |    0
 source/sharedochiai.cpp => sharedochiai.cpp   |    0
 source/sharedochiai.h => sharedochiai.h       |    0
 ...edordervector.cpp => sharedordervector.cpp |    0
 ...sharedordervector.h => sharedordervector.h |    0
 ...tvector.cpp => sharedrabundfloatvector.cpp |    0
 ...floatvector.h => sharedrabundfloatvector.h |    0
 ...rabundvector.cpp => sharedrabundvector.cpp |    0
 ...aredrabundvector.h => sharedrabundvector.h |    0
 ...sabundvector.cpp => sharedsabundvector.cpp |    0
 ...aredsabundvector.h => sharedsabundvector.h |    0
 source/sharedsobs.cpp => sharedsobs.cpp       |    0
 source/sharedsobs.h => sharedsobs.h           |    0
 ...ummary.cpp => sharedsobscollectsummary.cpp |    0
 ...ectsummary.h => sharedsobscollectsummary.h |    0
 .../sharedsorabund.cpp => sharedsorabund.cpp  |    0
 source/sharedsorabund.h => sharedsorabund.h   |    0
 .../sharedsorclass.cpp => sharedsorclass.cpp  |    0
 source/sharedsorclass.h => sharedsorclass.h   |    0
 source/sharedsorest.cpp => sharedsorest.cpp   |    0
 source/sharedsorest.h => sharedsorest.h       |    0
 source/sharedthetan.cpp => sharedthetan.cpp   |    0
 source/sharedthetan.h => sharedthetan.h       |    0
 source/sharedthetayc.cpp => sharedthetayc.cpp |    0
 source/sharedthetayc.h => sharedthetayc.h     |    0
 ...sharedutilities.cpp => sharedutilities.cpp |    0
 source/sharedutilities.h => sharedutilities.h |    0
 source/shen.cpp => shen.cpp                   |    0
 source/shen.h => shen.h                       |    0
 source/shhhercommand.cpp => shhhercommand.cpp |    0
 source/shhhercommand.h => shhhercommand.h     |    0
 ...shhhseqscommand.cpp => shhhseqscommand.cpp |    0
 source/shhhseqscommand.h => shhhseqscommand.h |    0
 source/simpson.cpp => simpson.cpp             |    0
 source/simpson.h => simpson.h                 |    0
 source/simpsoneven.cpp => simpsoneven.cpp     |    0
 source/simpsoneven.h => simpsoneven.h         |    0
 source/sinerp.f => sinerp.f                   |    0
 source/singlelinkage.cpp => singlelinkage.cpp |    0
 source/slayer.cpp => slayer.cpp               |    0
 source/slayer.h => slayer.h                   |    0
 source/slibshuff.cpp => slibshuff.cpp         |    0
 source/slibshuff.h => slibshuff.h             |    0
 source/smithwilson.cpp => smithwilson.cpp     |    0
 source/smithwilson.h => smithwilson.h         |    0
 source/sobs.h => sobs.h                       |    0
 source/soergel.cpp => soergel.cpp             |    0
 source/soergel.h => soergel.h                 |    0
 source/solow.cpp => solow.cpp                 |    0
 source/solow.h => solow.h                     |    0
 ...sortseqscommand.cpp => sortseqscommand.cpp |    0
 source/sortseqscommand.h => sortseqscommand.h |    0
 source/sparsematrix.cpp => sparsematrix.cpp   |    0
 source/sparsematrix.hpp => sparsematrix.hpp   |    0
 source/spearman.cpp => spearman.cpp           |    0
 source/spearman.h => spearman.h               |    0
 .../speciesprofile.cpp => speciesprofile.cpp  |    0
 source/speciesprofile.h => speciesprofile.h   |    0
 source/spline.cpp => spline.cpp               |    0
 source/spline.h => spline.h                   |    0
 ...tabundcommand.cpp => splitabundcommand.cpp |    0
 ...splitabundcommand.h => splitabundcommand.h |    0
 ...roupscommand.cpp => splitgroupscommand.cpp |    0
 ...litgroupscommand.h => splitgroupscommand.h |    0
 source/splitmatrix.cpp => splitmatrix.cpp     |    0
 source/splitmatrix.h => splitmatrix.h         |    0
 source/sslvrg.f => sslvrg.f                   |    0
 source/structchi2.cpp => structchi2.cpp       |    0
 source/structchi2.h => structchi2.h           |    0
 source/structchord.cpp => structchord.cpp     |    0
 source/structchord.h => structchord.h         |    0
 ...structeuclidean.cpp => structeuclidean.cpp |    0
 source/structeuclidean.h => structeuclidean.h |    0
 ...ructkulczynski.cpp => structkulczynski.cpp |    0
 .../structkulczynski.h => structkulczynski.h  |    0
 source/structpearson.cpp => structpearson.cpp |    0
 source/structpearson.h => structpearson.h     |    0
 source/stxwx.f => stxwx.f                     |    0
 source/subsample.cpp => subsample.cpp         |    0
 source/subsample.h => subsample.h             |    0
 ...bsamplecommand.cpp => subsamplecommand.cpp |    0
 .../subsamplecommand.h => subsamplecommand.h  |    0
 source/suffixdb.cpp => suffixdb.cpp           |    0
 source/suffixdb.hpp => suffixdb.hpp           |    0
 source/suffixnodes.cpp => suffixnodes.cpp     |    0
 source/suffixnodes.hpp => suffixnodes.hpp     |    0
 source/suffixtree.cpp => suffixtree.cpp       |    0
 source/suffixtree.hpp => suffixtree.hpp       |    0
 .../summarycommand.cpp => summarycommand.cpp  |    0
 source/summarycommand.h => summarycommand.h   |    0
 ...yqualcommand.cpp => summaryqualcommand.cpp |    0
 ...mmaryqualcommand.h => summaryqualcommand.h |    0
 ...redcommand.cpp => summarysharedcommand.cpp |    0
 ...ysharedcommand.h => summarysharedcommand.h |    0
 ...arytaxcommand.cpp => summarytaxcommand.cpp |    0
 ...summarytaxcommand.h => summarytaxcommand.h |    0
 source/systemcommand.cpp => systemcommand.cpp |    0
 source/systemcommand.h => systemcommand.h     |    0
 ...nomyequalizer.cpp => taxonomyequalizer.cpp |    0
 ...taxonomyequalizer.h => taxonomyequalizer.h |    0
 source/tree.cpp => tree.cpp                   |    0
 source/tree.h => tree.h                       |    0
 source/treecalculator.h => treecalculator.h   |    0
 ...groupscommand.cpp => treegroupscommand.cpp |    0
 ...treegroupscommand.h => treegroupscommand.h |    0
 source/treemap.cpp => treemap.cpp             |    0
 source/treemap.h => treemap.h                 |    0
 source/treenode.cpp => treenode.cpp           |    0
 source/treenode.h => treenode.h               |    0
 source/treereader.cpp => treereader.cpp       |    0
 source/treereader.h => treereader.h           |    0
 source/trialSwap2.cpp => trialSwap2.cpp       |    0
 source/trialswap2.h => trialswap2.h           |    0
 ...imflowscommand.cpp => trimflowscommand.cpp |    0
 .../trimflowscommand.h => trimflowscommand.h  |    0
 source/trimoligos.cpp => trimoligos.cpp       |    0
 source/trimoligos.h => trimoligos.h           |    0
 ...trimseqscommand.cpp => trimseqscommand.cpp |    0
 source/trimseqscommand.h => trimseqscommand.h |    0
 ...ommand.cpp => unifracunweightedcommand.cpp |    0
 ...tedcommand.h => unifracunweightedcommand.h |    0
 ...dcommand.cpp => unifracweightedcommand.cpp |    0
 ...ghtedcommand.h => unifracweightedcommand.h |    0
 source/unweighted.cpp => unweighted.cpp       |    0
 source/unweighted.h => unweighted.h           |    0
 source/uvest.cpp => uvest.cpp                 |    0
 source/uvest.h => uvest.h                     |    0
 ...validcalculator.cpp => validcalculator.cpp |    0
 source/validcalculator.h => validcalculator.h |    0
 .../validparameter.cpp => validparameter.cpp  |    0
 source/validparameter.h => validparameter.h   |    0
 source/venn.cpp => venn.cpp                   |    0
 source/venn.h => venn.h                       |    0
 source/venncommand.cpp => venncommand.cpp     |    0
 source/venncommand.h => venncommand.h         |    0
 source/weighted.cpp => weighted.cpp           |    0
 source/weighted.h => weighted.h               |    0
 ...weightedlinkage.cpp => weightedlinkage.cpp |    0
 source/whittaker.cpp => whittaker.cpp         |    0
 source/whittaker.h => whittaker.h             |    0
 651 files changed, 651 insertions(+), 651 deletions(-)
 rename source/ace.cpp => ace.cpp (100%)
 rename source/ace.h => ace.h (100%)
 rename source/aligncommand.cpp => aligncommand.cpp (100%)
 rename source/aligncommand.h => aligncommand.h (99%)
 rename source/alignment.cpp => alignment.cpp (100%)
 rename source/alignment.hpp => alignment.hpp (100%)
 rename source/alignmentcell.cpp => alignmentcell.cpp (100%)
 rename source/alignmentcell.hpp => alignmentcell.hpp (100%)
 rename source/alignmentdb.cpp => alignmentdb.cpp (100%)
 rename source/alignmentdb.h => alignmentdb.h (100%)
 rename source/amovacommand.cpp => amovacommand.cpp (100%)
 rename source/amovacommand.h => amovacommand.h (100%)
 rename source/anosimcommand.cpp => anosimcommand.cpp (100%)
 rename source/anosimcommand.h => anosimcommand.h (100%)
 rename source/averagelinkage.cpp => averagelinkage.cpp (100%)
 rename source/bayesian.cpp => bayesian.cpp (100%)
 rename source/bayesian.h => bayesian.h (100%)
 rename source/bellerophon.cpp => bellerophon.cpp (100%)
 rename source/bellerophon.h => bellerophon.h (100%)
 rename source/bergerparker.cpp => bergerparker.cpp (100%)
 rename source/bergerparker.h => bergerparker.h (100%)
 rename source/binsequencecommand.cpp => binsequencecommand.cpp (100%)
 rename source/binsequencecommand.h => binsequencecommand.h (100%)
 rename source/blastalign.cpp => blastalign.cpp (100%)
 rename source/blastalign.hpp => blastalign.hpp (100%)
 rename source/blastdb.cpp => blastdb.cpp (100%)
 rename source/blastdb.hpp => blastdb.hpp (100%)
 rename source/boneh.cpp => boneh.cpp (100%)
 rename source/boneh.h => boneh.h (100%)
 rename source/bootstrap.cpp => bootstrap.cpp (100%)
 rename source/bootstrap.h => bootstrap.h (100%)
 rename source/bsplvb.f => bsplvb.f (100%)
 rename source/bsplvd.f => bsplvd.f (100%)
 rename source/bstick.cpp => bstick.cpp (100%)
 rename source/bstick.h => bstick.h (100%)
 rename source/bvalue.f => bvalue.f (100%)
 rename source/calculator.cpp => calculator.cpp (100%)
 rename source/calculator.h => calculator.h (100%)
 rename source/canberra.cpp => canberra.cpp (100%)
 rename source/canberra.h => canberra.h (100%)
 rename source/catchallcommand.cpp => catchallcommand.cpp (100%)
 rename source/catchallcommand.h => catchallcommand.h (100%)
 rename source/ccode.cpp => ccode.cpp (100%)
 rename source/ccode.h => ccode.h (100%)
 rename source/chao1.cpp => chao1.cpp (100%)
 rename source/chao1.h => chao1.h (100%)
 rename source/chimera.cpp => chimera.cpp (100%)
 rename source/chimera.h => chimera.h (100%)
 rename source/chimerabellerophoncommand.cpp => chimerabellerophoncommand.cpp (100%)
 rename source/chimerabellerophoncommand.h => chimerabellerophoncommand.h (100%)
 rename source/chimeraccodecommand.cpp => chimeraccodecommand.cpp (100%)
 rename source/chimeraccodecommand.h => chimeraccodecommand.h (100%)
 rename source/chimeracheckcommand.cpp => chimeracheckcommand.cpp (100%)
 rename source/chimeracheckcommand.h => chimeracheckcommand.h (100%)
 rename source/chimeracheckrdp.cpp => chimeracheckrdp.cpp (100%)
 rename source/chimeracheckrdp.h => chimeracheckrdp.h (100%)
 rename source/chimeraperseuscommand.cpp => chimeraperseuscommand.cpp (100%)
 rename source/chimeraperseuscommand.h => chimeraperseuscommand.h (100%)
 rename source/chimerapintailcommand.cpp => chimerapintailcommand.cpp (100%)
 rename source/chimerapintailcommand.h => chimerapintailcommand.h (100%)
 rename source/chimerarealigner.cpp => chimerarealigner.cpp (100%)
 rename source/chimerarealigner.h => chimerarealigner.h (100%)
 rename source/chimeraslayer.cpp => chimeraslayer.cpp (100%)
 rename source/chimeraslayer.h => chimeraslayer.h (100%)
 rename source/chimeraslayercommand.cpp => chimeraslayercommand.cpp (100%)
 rename source/chimeraslayercommand.h => chimeraslayercommand.h (100%)
 rename source/chimerauchimecommand.cpp => chimerauchimecommand.cpp (100%)
 rename source/chimerauchimecommand.h => chimerauchimecommand.h (100%)
 rename source/chopseqscommand.cpp => chopseqscommand.cpp (100%)
 rename source/chopseqscommand.h => chopseqscommand.h (100%)
 rename source/classify.cpp => classify.cpp (100%)
 rename source/classify.h => classify.h (100%)
 rename source/classifyotucommand.cpp => classifyotucommand.cpp (100%)
 rename source/classifyotucommand.h => classifyotucommand.h (100%)
 rename source/classifyseqscommand.cpp => classifyseqscommand.cpp (100%)
 rename source/classifyseqscommand.h => classifyseqscommand.h (100%)
 rename source/classifytreecommand.cpp => classifytreecommand.cpp (100%)
 rename source/classifytreecommand.h => classifytreecommand.h (100%)
 rename source/clearcut.cpp => clearcut.cpp (100%)
 rename source/clearcut.h => clearcut.h (100%)
 rename source/clearcutcommand.cpp => clearcutcommand.cpp (100%)
 rename source/clearcutcommand.h => clearcutcommand.h (100%)
 rename source/clearmemorycommand.cpp => clearmemorycommand.cpp (100%)
 rename source/clearmemorycommand.h => clearmemorycommand.h (100%)
 rename source/cluster.cpp => cluster.cpp (100%)
 rename source/cluster.hpp => cluster.hpp (100%)
 rename source/clusterclassic.cpp => clusterclassic.cpp (100%)
 rename source/clusterclassic.h => clusterclassic.h (100%)
 rename source/clustercommand.cpp => clustercommand.cpp (100%)
 rename source/clustercommand.h => clustercommand.h (100%)
 rename source/clusterdoturcommand.cpp => clusterdoturcommand.cpp (100%)
 rename source/clusterdoturcommand.h => clusterdoturcommand.h (100%)
 rename source/clusterfragmentscommand.cpp => clusterfragmentscommand.cpp (100%)
 rename source/clusterfragmentscommand.h => clusterfragmentscommand.h (100%)
 rename source/clustersplitcommand.cpp => clustersplitcommand.cpp (100%)
 rename source/clustersplitcommand.h => clustersplitcommand.h (100%)
 rename source/cmdargs.cpp => cmdargs.cpp (100%)
 rename source/cmdargs.h => cmdargs.h (100%)
 rename source/collect.cpp => collect.cpp (100%)
 rename source/collect.h => collect.h (100%)
 rename source/collectcommand.cpp => collectcommand.cpp (100%)
 rename source/collectcommand.h => collectcommand.h (100%)
 rename source/collectdisplay.h => collectdisplay.h (100%)
 rename source/collectorscurvedata.h => collectorscurvedata.h (100%)
 rename source/collectsharedcommand.cpp => collectsharedcommand.cpp (100%)
 rename source/collectsharedcommand.h => collectsharedcommand.h (100%)
 rename source/command.hpp => command.hpp (100%)
 rename source/commandfactory.cpp => commandfactory.cpp (100%)
 rename source/commandfactory.hpp => commandfactory.hpp (100%)
 rename source/commandoptionparser.cpp => commandoptionparser.cpp (100%)
 rename source/commandoptionparser.hpp => commandoptionparser.hpp (100%)
 rename source/commandparameter.h => commandparameter.h (100%)
 rename source/common.h => common.h (100%)
 rename source/completelinkage.cpp => completelinkage.cpp (100%)
 rename source/consensus.cpp => consensus.cpp (100%)
 rename source/consensus.h => consensus.h (100%)
 rename source/consensusseqscommand.cpp => consensusseqscommand.cpp (100%)
 rename source/consensusseqscommand.h => consensusseqscommand.h (100%)
 rename source/cooccurrencecommand.cpp => cooccurrencecommand.cpp (100%)
 rename source/cooccurrencecommand.h => cooccurrencecommand.h (100%)
 rename source/corraxescommand.cpp => corraxescommand.cpp (100%)
 rename source/corraxescommand.h => corraxescommand.h (100%)
 rename source/countgroupscommand.cpp => countgroupscommand.cpp (100%)
 rename source/countgroupscommand.h => countgroupscommand.h (100%)
 rename source/countseqscommand.cpp => countseqscommand.cpp (100%)
 rename source/countseqscommand.h => countseqscommand.h (100%)
 rename source/coverage.cpp => coverage.cpp (100%)
 rename source/coverage.h => coverage.h (100%)
 rename source/createdatabasecommand.cpp => createdatabasecommand.cpp (100%)
 rename source/createdatabasecommand.h => createdatabasecommand.h (100%)
 rename source/currentfile.h => currentfile.h (100%)
 rename source/database.cpp => database.cpp (100%)
 rename source/database.hpp => database.hpp (100%)
 rename source/datavector.hpp => datavector.hpp (100%)
 rename source/daxpy.f => daxpy.f (100%)
 rename source/dayhoff.h => dayhoff.h (100%)
 rename source/ddot.f => ddot.f (100%)
 rename source/decalc.cpp => decalc.cpp (100%)
 rename source/decalc.h => decalc.h (100%)
 rename source/deconvolutecommand.cpp => deconvolutecommand.cpp (100%)
 rename source/deconvolutecommand.h => deconvolutecommand.h (100%)
 rename source/degapseqscommand.cpp => degapseqscommand.cpp (100%)
 rename source/degapseqscommand.h => degapseqscommand.h (100%)
 rename source/deuniqueseqscommand.cpp => deuniqueseqscommand.cpp (100%)
 rename source/deuniqueseqscommand.h => deuniqueseqscommand.h (100%)
 rename source/deuniquetreecommand.cpp => deuniquetreecommand.cpp (100%)
 rename source/deuniquetreecommand.h => deuniquetreecommand.h (100%)
 rename source/display.h => display.h (100%)
 rename source/dist.h => dist.h (100%)
 rename source/distancecommand.cpp => distancecommand.cpp (100%)
 rename source/distancecommand.h => distancecommand.h (100%)
 rename source/distancedb.cpp => distancedb.cpp (100%)
 rename source/distancedb.hpp => distancedb.hpp (100%)
 rename source/distclearcut.cpp => distclearcut.cpp (100%)
 rename source/distclearcut.h => distclearcut.h (100%)
 rename source/dlibshuff.cpp => dlibshuff.cpp (100%)
 rename source/dlibshuff.h => dlibshuff.h (100%)
 rename source/dmat.cpp => dmat.cpp (100%)
 rename source/dmat.h => dmat.h (100%)
 rename source/dpbfa.f => dpbfa.f (100%)
 rename source/dpbsl.f => dpbsl.f (100%)
 rename source/eachgapdist.h => eachgapdist.h (100%)
 rename source/eachgapdistignorens.h => eachgapdistignorens.h (100%)
 rename source/eachgapignore.h => eachgapignore.h (100%)
 rename source/efron.cpp => efron.cpp (100%)
 rename source/efron.h => efron.h (100%)
 rename source/endiannessmacros.h => endiannessmacros.h (100%)
 rename source/engine.cpp => engine.cpp (100%)
 rename source/engine.hpp => engine.hpp (100%)
 rename source/fasta.cpp => fasta.cpp (100%)
 rename source/fasta.h => fasta.h (100%)
 rename source/fastamap.cpp => fastamap.cpp (100%)
 rename source/fastamap.h => fastamap.h (100%)
 rename source/fileoutput.cpp => fileoutput.cpp (100%)
 rename source/fileoutput.h => fileoutput.h (100%)
 rename source/filters.h => filters.h (100%)
 rename source/filterseqscommand.cpp => filterseqscommand.cpp (100%)
 rename source/filterseqscommand.h => filterseqscommand.h (100%)
 rename source/flowdata.cpp => flowdata.cpp (100%)
 rename source/flowdata.h => flowdata.h (100%)
 rename source/formatcolumn.cpp => formatcolumn.cpp (100%)
 rename source/formatcolumn.h => formatcolumn.h (100%)
 rename source/formatmatrix.h => formatmatrix.h (100%)
 rename source/formatphylip.cpp => formatphylip.cpp (100%)
 rename source/formatphylip.h => formatphylip.h (100%)
 rename source/fullmatrix.cpp => fullmatrix.cpp (100%)
 rename source/fullmatrix.h => fullmatrix.h (100%)
 rename source/geom.cpp => geom.cpp (100%)
 rename source/geom.h => geom.h (100%)
 rename source/getcommandinfocommand.cpp => getcommandinfocommand.cpp (100%)
 rename source/getcommandinfocommand.h => getcommandinfocommand.h (100%)
 rename source/getcurrentcommand.cpp => getcurrentcommand.cpp (100%)
 rename source/getcurrentcommand.h => getcurrentcommand.h (100%)
 rename source/getgroupcommand.cpp => getgroupcommand.cpp (100%)
 rename source/getgroupcommand.h => getgroupcommand.h (100%)
 rename source/getgroupscommand.cpp => getgroupscommand.cpp (100%)
 rename source/getgroupscommand.h => getgroupscommand.h (100%)
 rename source/getlabelcommand.cpp => getlabelcommand.cpp (100%)
 rename source/getlabelcommand.h => getlabelcommand.h (100%)
 rename source/getlineagecommand.cpp => getlineagecommand.cpp (100%)
 rename source/getlineagecommand.h => getlineagecommand.h (100%)
 rename source/getlistcountcommand.cpp => getlistcountcommand.cpp (100%)
 rename source/getlistcountcommand.h => getlistcountcommand.h (100%)
 rename source/getopt_long.cpp => getopt_long.cpp (100%)
 rename source/getopt_long.h => getopt_long.h (100%)
 rename source/getoturepcommand.cpp => getoturepcommand.cpp (100%)
 rename source/getoturepcommand.h => getoturepcommand.h (100%)
 rename source/getotuscommand.cpp => getotuscommand.cpp (100%)
 rename source/getotuscommand.h => getotuscommand.h (100%)
 rename source/getrabundcommand.cpp => getrabundcommand.cpp (100%)
 rename source/getrabundcommand.h => getrabundcommand.h (100%)
 rename source/getrelabundcommand.cpp => getrelabundcommand.cpp (100%)
 rename source/getrelabundcommand.h => getrelabundcommand.h (100%)
 rename source/getsabundcommand.cpp => getsabundcommand.cpp (100%)
 rename source/getsabundcommand.h => getsabundcommand.h (100%)
 rename source/getseqscommand.cpp => getseqscommand.cpp (100%)
 rename source/getseqscommand.h => getseqscommand.h (100%)
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 rename source/unweighted.cpp => unweighted.cpp (100%)
 rename source/unweighted.h => unweighted.h (100%)
 rename source/uvest.cpp => uvest.cpp (100%)
 rename source/uvest.h => uvest.h (100%)
 rename source/validcalculator.cpp => validcalculator.cpp (100%)
 rename source/validcalculator.h => validcalculator.h (100%)
 rename source/validparameter.cpp => validparameter.cpp (100%)
 rename source/validparameter.h => validparameter.h (100%)
 rename source/venn.cpp => venn.cpp (100%)
 rename source/venn.h => venn.h (100%)
 rename source/venncommand.cpp => venncommand.cpp (100%)
 rename source/venncommand.h => venncommand.h (100%)
 rename source/weighted.cpp => weighted.cpp (100%)
 rename source/weighted.h => weighted.h (100%)
 rename source/weightedlinkage.cpp => weightedlinkage.cpp (100%)
 rename source/whittaker.cpp => whittaker.cpp (100%)
 rename source/whittaker.h => whittaker.h (100%)

diff --git a/Mothur.xcodeproj/project.pbxproj b/Mothur.xcodeproj/project.pbxproj
index f62b9b4..6e156df 100644
--- a/Mothur.xcodeproj/project.pbxproj
+++ b/Mothur.xcodeproj/project.pbxproj
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diff --git a/source/ace.cpp b/ace.cpp
similarity index 100%
rename from source/ace.cpp
rename to ace.cpp
diff --git a/source/ace.h b/ace.h
similarity index 100%
rename from source/ace.h
rename to ace.h
diff --git a/source/aligncommand.cpp b/aligncommand.cpp
similarity index 100%
rename from source/aligncommand.cpp
rename to aligncommand.cpp
diff --git a/source/aligncommand.h b/aligncommand.h
similarity index 99%
rename from source/aligncommand.h
rename to aligncommand.h
index c7ce144..5da7a1f 100644
--- a/source/aligncommand.h
+++ b/aligncommand.h
@@ -1,6 +1,6 @@
 #ifndef ALIGNCOMMAND_H
 #define ALIGNCOMMAND_H
-
+//test
 /*
  *  aligncommand.h
  *  Mothur
diff --git a/source/alignment.cpp b/alignment.cpp
similarity index 100%
rename from source/alignment.cpp
rename to alignment.cpp
diff --git a/source/alignment.hpp b/alignment.hpp
similarity index 100%
rename from source/alignment.hpp
rename to alignment.hpp
diff --git a/source/alignmentcell.cpp b/alignmentcell.cpp
similarity index 100%
rename from source/alignmentcell.cpp
rename to alignmentcell.cpp
diff --git a/source/alignmentcell.hpp b/alignmentcell.hpp
similarity index 100%
rename from source/alignmentcell.hpp
rename to alignmentcell.hpp
diff --git a/source/alignmentdb.cpp b/alignmentdb.cpp
similarity index 100%
rename from source/alignmentdb.cpp
rename to alignmentdb.cpp
diff --git a/source/alignmentdb.h b/alignmentdb.h
similarity index 100%
rename from source/alignmentdb.h
rename to alignmentdb.h
diff --git a/source/amovacommand.cpp b/amovacommand.cpp
similarity index 100%
rename from source/amovacommand.cpp
rename to amovacommand.cpp
diff --git a/source/amovacommand.h b/amovacommand.h
similarity index 100%
rename from source/amovacommand.h
rename to amovacommand.h
diff --git a/source/anosimcommand.cpp b/anosimcommand.cpp
similarity index 100%
rename from source/anosimcommand.cpp
rename to anosimcommand.cpp
diff --git a/source/anosimcommand.h b/anosimcommand.h
similarity index 100%
rename from source/anosimcommand.h
rename to anosimcommand.h
diff --git a/source/averagelinkage.cpp b/averagelinkage.cpp
similarity index 100%
rename from source/averagelinkage.cpp
rename to averagelinkage.cpp
diff --git a/source/bayesian.cpp b/bayesian.cpp
similarity index 100%
rename from source/bayesian.cpp
rename to bayesian.cpp
diff --git a/source/bayesian.h b/bayesian.h
similarity index 100%
rename from source/bayesian.h
rename to bayesian.h
diff --git a/source/bellerophon.cpp b/bellerophon.cpp
similarity index 100%
rename from source/bellerophon.cpp
rename to bellerophon.cpp
diff --git a/source/bellerophon.h b/bellerophon.h
similarity index 100%
rename from source/bellerophon.h
rename to bellerophon.h
diff --git a/source/bergerparker.cpp b/bergerparker.cpp
similarity index 100%
rename from source/bergerparker.cpp
rename to bergerparker.cpp
diff --git a/source/bergerparker.h b/bergerparker.h
similarity index 100%
rename from source/bergerparker.h
rename to bergerparker.h
diff --git a/source/binsequencecommand.cpp b/binsequencecommand.cpp
similarity index 100%
rename from source/binsequencecommand.cpp
rename to binsequencecommand.cpp
diff --git a/source/binsequencecommand.h b/binsequencecommand.h
similarity index 100%
rename from source/binsequencecommand.h
rename to binsequencecommand.h
diff --git a/source/blastalign.cpp b/blastalign.cpp
similarity index 100%
rename from source/blastalign.cpp
rename to blastalign.cpp
diff --git a/source/blastalign.hpp b/blastalign.hpp
similarity index 100%
rename from source/blastalign.hpp
rename to blastalign.hpp
diff --git a/source/blastdb.cpp b/blastdb.cpp
similarity index 100%
rename from source/blastdb.cpp
rename to blastdb.cpp
diff --git a/source/blastdb.hpp b/blastdb.hpp
similarity index 100%
rename from source/blastdb.hpp
rename to blastdb.hpp
diff --git a/source/boneh.cpp b/boneh.cpp
similarity index 100%
rename from source/boneh.cpp
rename to boneh.cpp
diff --git a/source/boneh.h b/boneh.h
similarity index 100%
rename from source/boneh.h
rename to boneh.h
diff --git a/source/bootstrap.cpp b/bootstrap.cpp
similarity index 100%
rename from source/bootstrap.cpp
rename to bootstrap.cpp
diff --git a/source/bootstrap.h b/bootstrap.h
similarity index 100%
rename from source/bootstrap.h
rename to bootstrap.h
diff --git a/source/bsplvb.f b/bsplvb.f
similarity index 100%
rename from source/bsplvb.f
rename to bsplvb.f
diff --git a/source/bsplvd.f b/bsplvd.f
similarity index 100%
rename from source/bsplvd.f
rename to bsplvd.f
diff --git a/source/bstick.cpp b/bstick.cpp
similarity index 100%
rename from source/bstick.cpp
rename to bstick.cpp
diff --git a/source/bstick.h b/bstick.h
similarity index 100%
rename from source/bstick.h
rename to bstick.h
diff --git a/source/bvalue.f b/bvalue.f
similarity index 100%
rename from source/bvalue.f
rename to bvalue.f
diff --git a/source/calculator.cpp b/calculator.cpp
similarity index 100%
rename from source/calculator.cpp
rename to calculator.cpp
diff --git a/source/calculator.h b/calculator.h
similarity index 100%
rename from source/calculator.h
rename to calculator.h
diff --git a/source/canberra.cpp b/canberra.cpp
similarity index 100%
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diff --git a/source/weightedlinkage.cpp b/weightedlinkage.cpp
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diff --git a/source/whittaker.cpp b/whittaker.cpp
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-- 
2.39.2