This is GSoC2012 fork of 'Mothur'. We are trying to implement a number of 'Feature Selection' algorithms for microbial ecology data and incorporate them into mother's main codebase.
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.settings
Mothur.xcodeproj
fs
uchime_src
.cproject
.gitignore
.project
LICENSE
LookUp_GS20.pat
LookUp_GSFLX.pat
LookUp_Titanium.pat
Mothur.1
abstractdecisiontree.cpp
abstractdecisiontree.hpp
ace.cpp
ace.h
aligncommand.cpp
aligncommand.h
alignment.cpp
alignment.hpp
alignmentcell.cpp
alignmentcell.hpp
alignmentdb.cpp
alignmentdb.h
alignnode.cpp
alignnode.h
aligntree.cpp
aligntree.h
amovacommand.cpp
amovacommand.h
anosimcommand.cpp
anosimcommand.h
averagelinkage.cpp
bayesian.cpp
bayesian.h
bellerophon.cpp
bellerophon.h
bergerparker.cpp
bergerparker.h
binsequencecommand.cpp
binsequencecommand.h
blastalign.cpp
blastalign.hpp
blastdb.cpp
blastdb.hpp
boneh.cpp
boneh.h
bootstrap.cpp
bootstrap.h
bsplvb.f
bsplvd.f
bstick.cpp
bstick.h
bvalue.f
calcsparcc.cpp
calcsparcc.h
calculator.cpp
calculator.h
canberra.cpp
canberra.h
catchallcommand.cpp
catchallcommand.h
ccode.cpp
ccode.h
chao1.cpp
chao1.h
chimera.cpp
chimera.h
chimerabellerophoncommand.cpp
chimerabellerophoncommand.h
chimeraccodecommand.cpp
chimeraccodecommand.h
chimeracheckcommand.cpp
chimeracheckcommand.h
chimeracheckrdp.cpp
chimeracheckrdp.h
chimeraperseuscommand.cpp
chimeraperseuscommand.h
chimerapintailcommand.cpp
chimerapintailcommand.h
chimerarealigner.cpp
chimerarealigner.h
chimeraslayer.cpp
chimeraslayer.h
chimeraslayercommand.cpp
chimeraslayercommand.h
chimerauchimecommand.cpp
chimerauchimecommand.h
chopseqscommand.cpp
chopseqscommand.h
classify.cpp
classify.h
classifyotucommand.cpp
classifyotucommand.h
classifyseqscommand.cpp
classifyseqscommand.h
classifysharedcommand.cpp
classifysharedcommand.h
classifytreecommand.cpp
classifytreecommand.h
clearcut.cpp
clearcut.h
clearcutcommand.cpp
clearcutcommand.h
clearmemorycommand.cpp
clearmemorycommand.h
cluster.cpp
cluster.hpp
clusterclassic.cpp
clusterclassic.h
clustercommand.cpp
clustercommand.h
clusterdoturcommand.cpp
clusterdoturcommand.h
clusterfragmentscommand.cpp
clusterfragmentscommand.h
clustersplitcommand.cpp
clustersplitcommand.h
cmdargs.cpp
cmdargs.h
collect.cpp
collect.h
collectcommand.cpp
collectcommand.h
collectdisplay.h
collectorscurvedata.h
collectsharedcommand.cpp
collectsharedcommand.h
command.hpp
commandfactory.cpp
commandfactory.hpp
commandoptionparser.cpp
commandoptionparser.hpp
commandparameter.h
common.h
completelinkage.cpp
consensus.cpp
consensus.h
consensusseqscommand.cpp
consensusseqscommand.h
cooccurrencecommand.cpp
cooccurrencecommand.h
corraxescommand.cpp
corraxescommand.h
countgroupscommand.cpp
countgroupscommand.h
countseqscommand.cpp
countseqscommand.h
counttable.cpp
counttable.h
coverage.cpp
coverage.h
createdatabasecommand.cpp
createdatabasecommand.h
currentfile.h
database.cpp
database.hpp
datavector.hpp
daxpy.f
dayhoff.h
ddot.f
decalc.cpp
decalc.h
decisiontree.cpp
decisiontree.hpp
deconvolutecommand.cpp
deconvolutecommand.h
degapseqscommand.cpp
degapseqscommand.h
designmap.cpp
designmap.h
deuniqueseqscommand.cpp
deuniqueseqscommand.h
deuniquetreecommand.cpp
deuniquetreecommand.h
display.h
dist.h
distancecommand.cpp
distancecommand.h
distancedb.cpp
distancedb.hpp
distclearcut.cpp
distclearcut.h
dlibshuff.cpp
dlibshuff.h
dmat.cpp
dmat.h
dpbfa.f
dpbsl.f
eachgapdist.h
eachgapdistignorens.h
eachgapignore.h
efron.cpp
efron.h
endiannessmacros.h
engine.cpp
engine.hpp
fasta.cpp
fasta.h
fastamap.cpp
fastamap.h
fileoutput.cpp
fileoutput.h
filters.h
filterseqscommand.cpp
filterseqscommand.h
filtersharedcommand.cpp
filtersharedcommand.h
flowdata.cpp
flowdata.h
forest.cpp
forest.h
formatcolumn.cpp
formatcolumn.h
formatmatrix.h
formatphylip.cpp
formatphylip.h
fullmatrix.cpp
fullmatrix.h
geom.cpp
geom.h
getcommandinfocommand.cpp
getcommandinfocommand.h
getcoremicrobiomecommand.cpp
getcoremicrobiomecommand.h
getcurrentcommand.cpp
getcurrentcommand.h
getdistscommand.cpp
getdistscommand.h
getgroupcommand.cpp
getgroupcommand.h
getgroupscommand.cpp
getgroupscommand.h
getlabelcommand.cpp
getlabelcommand.h
getlineagecommand.cpp
getlineagecommand.h
getlistcountcommand.cpp
getlistcountcommand.h
getmetacommunitycommand.cpp
getmetacommunitycommand.h
getopt_long.cpp
getopt_long.h
getotulabelscommand.cpp
getotulabelscommand.h
getoturepcommand.cpp
getoturepcommand.h
getotuscommand.cpp
getotuscommand.h
getrabundcommand.cpp
getrabundcommand.h
getrelabundcommand.cpp
getrelabundcommand.h
getsabundcommand.cpp
getsabundcommand.h
getseqscommand.cpp
getseqscommand.h
getsharedotucommand.cpp
getsharedotucommand.h
goodscoverage.cpp
goodscoverage.h
gotohoverlap.cpp
gotohoverlap.hpp
gower.cpp
gower.h
groupmap.cpp
groupmap.h
hamming.cpp
hamming.h
hcluster.cpp
hcluster.h
hclustercommand.cpp
hclustercommand.h
heatmap.cpp
heatmap.h
heatmapcommand.cpp
heatmapcommand.h
heatmapsim.cpp
heatmapsim.h
heatmapsimcommand.cpp
heatmapsimcommand.h
heip.cpp
heip.h
hellinger.cpp
hellinger.h
helpcommand.cpp
helpcommand.h
homovacommand.cpp
homovacommand.h
ignoregaps.h
indicatorcommand.cpp
indicatorcommand.h
inputdata.cpp
inputdata.h
interv.f
intrv.f
invsimpson.cpp
invsimpson.h
jackknife.cpp
jackknife.h
kmer.cpp
kmer.hpp
kmerdb.cpp
kmerdb.hpp
kmernode.cpp
kmernode.h
kmertree.cpp
kmertree.h
knn.cpp
knn.h
kruskalwalliscommand.cpp
kruskalwalliscommand.h
lefsecommand.cpp
lefsecommand.h
libshuff.cpp
libshuff.h
libshuffcommand.cpp
libshuffcommand.h
linearalgebra.cpp
linearalgebra.h
listotulabelscommand.cpp
listotulabelscommand.h
listseqscommand.cpp
listseqscommand.h
listvector.cpp
listvector.hpp
loadlogfilecommand.cpp
loadlogfilecommand.h
logsd.cpp
logsd.h
macros.h
makebiomcommand.cpp
makebiomcommand.h
makecontigscommand.cpp
makecontigscommand.h
makefastqcommand.cpp
makefastqcommand.h
makefile
makegroupcommand.cpp
makegroupcommand.h
makelefsecommand.cpp
makelefsecommand.h
makelookupcommand.cpp
makelookupcommand.h
maligner.cpp
maligner.h
manhattan.cpp
manhattan.h
mantelcommand.cpp
mantelcommand.h
matrixoutputcommand.cpp
matrixoutputcommand.h
memchi2.cpp
memchi2.h
memchord.cpp
memchord.h
memeuclidean.cpp
memeuclidean.h
mempearson.cpp
mempearson.h
mergefilecommand.cpp
mergefilecommand.h
mergegroupscommand.cpp
mergegroupscommand.h
mergetaxsummarycommand.cpp
mergetaxsummarycommand.h
metastatscommand.cpp
metastatscommand.h
mgclustercommand.cpp
mgclustercommand.h
mothur.cpp
mothur.h
mothurfisher.cpp
mothurfisher.h
mothurmetastats.cpp
mothurmetastats.h
mothurout.cpp
mothurout.h
myPerseus.cpp
myPerseus.h
myseqdist.cpp
myseqdist.h
nameassignment.cpp
nameassignment.hpp
nast.cpp
nast.hpp
nastreport.cpp
nastreport.hpp
needlemanoverlap.cpp
needlemanoverlap.hpp
newcommandtemplate.cpp
newcommandtemplate.h
nmdscommand.cpp
nmdscommand.h
noalign.cpp
noalign.hpp
nocommands.cpp
nocommands.h
normalizesharedcommand.cpp
normalizesharedcommand.h
npshannon.cpp
npshannon.h
nseqs.h
observable.h
odum.cpp
odum.h
onegapdist.h
onegapignore.h
optionparser.cpp
optionparser.h
ordervector.cpp
ordervector.hpp
otuassociationcommand.cpp
otuassociationcommand.h
otuhierarchycommand.cpp
otuhierarchycommand.h
overlap.cpp
overlap.hpp
pairwiseseqscommand.cpp
pairwiseseqscommand.h
parsefastaqcommand.cpp
parsefastaqcommand.h
parselistscommand.cpp
parselistscommand.h
parsimony.cpp
parsimony.h
parsimonycommand.cpp
parsimonycommand.h
pcacommand.cpp
pcacommand.h
pcoacommand.cpp
pcoacommand.h
pcrseqscommand.h
phylodiversitycommand.cpp
phylodiversitycommand.h
phylosummary.cpp
phylosummary.h
phylotree.cpp
phylotree.h
phylotypecommand.cpp
phylotypecommand.h
pintail.cpp
pintail.h
pipelinepdscommand.cpp
pipelinepdscommand.h
prcseqscommand.cpp
preclustercommand.cpp
preclustercommand.h
primerdesigncommand.cpp
primerdesigncommand.h
prng.cpp
prng.h
progress.cpp
progress.hpp
qFinderDMM.cpp
qFinderDMM.h
qstat.cpp
qstat.h
qualityscores.cpp
qualityscores.h
quitcommand.cpp
quitcommand.h
rabundvector.cpp
rabundvector.hpp
randomforest.cpp
randomforest.hpp
randomnumber.cpp
randomnumber.h
rarecalc.cpp
rarecalc.h
raredisplay.cpp
raredisplay.h
rarefact.cpp
rarefact.h
rarefactcommand.cpp
rarefactcommand.h
rarefactioncurvedata.h
rarefactsharedcommand.cpp
rarefactsharedcommand.h
readblast.cpp
readblast.h
readcluster.cpp
readcluster.h
readcolumn.cpp
readcolumn.h
readmatrix.hpp
readphylip.cpp
readphylip.h
readphylipvector.cpp
readphylipvector.h
readtree.cpp
readtree.h
refchimeratest.cpp
refchimeratest.h
referencedb.cpp
referencedb.h
regularizeddecisiontree.cpp
regularizeddecisiontree.h
regularizedrandomforest.cpp
regularizedrandomforest.h
removedistscommand.cpp
removedistscommand.h
removegroupscommand.cpp
removegroupscommand.h
removelineagecommand.cpp
removelineagecommand.h
removeotulabelscommand.cpp
removeotulabelscommand.h
removeotuscommand.cpp
removeotuscommand.h
removerarecommand.cpp
removerarecommand.h
removeseqscommand.cpp
removeseqscommand.h
renameseqscommand.cpp
renameseqscommand.h
reportfile.cpp
reportfile.h
reversecommand.cpp
reversecommand.h
rftreenode.cpp
rftreenode.hpp
sabundvector.cpp
sabundvector.hpp
screenseqscommand.cpp
screenseqscommand.h
secondarystructurecommand.cpp
secondarystructurecommand.h
sensspeccommand.cpp
sensspeccommand.h
seqerrorcommand.cpp
seqerrorcommand.h
seqnoise.cpp
seqnoise.h
seqsummarycommand.cpp
seqsummarycommand.h
sequence.cpp
sequence.hpp
sequencecountparser.cpp
sequencecountparser.h
sequencedb.cpp
sequencedb.h
sequenceparser.cpp
sequenceparser.h
setcurrentcommand.cpp
setcurrentcommand.h
setdircommand.cpp
setdircommand.h
setlogfilecommand.cpp
setlogfilecommand.h
sffinfocommand.cpp
sffinfocommand.h
sffmultiplecommand.cpp
sffmultiplecommand.h
sgram.f
shannon.cpp
shannon.h
shannoneven.cpp
shannoneven.h
sharedace.cpp
sharedace.h
sharedanderbergs.cpp
sharedanderbergs.h
sharedbraycurtis.cpp
sharedbraycurtis.h
sharedchao1.cpp
sharedchao1.h
sharedcommand.cpp
sharedcommand.h
sharedjabund.cpp
sharedjabund.h
sharedjackknife.cpp
sharedjackknife.h
sharedjclass.cpp
sharedjclass.h
sharedjest.cpp
sharedjest.h
sharedkstest.cpp
sharedkstest.h
sharedkulczynski.cpp
sharedkulczynski.h
sharedkulczynskicody.cpp
sharedkulczynskicody.h
sharedlennon.cpp
sharedlennon.h
sharedlistvector.cpp
sharedlistvector.h
sharedmarczewski.cpp
sharedmarczewski.h
sharedmorisitahorn.cpp
sharedmorisitahorn.h
sharednseqs.h
sharedochiai.cpp
sharedochiai.h
sharedordervector.cpp
sharedordervector.h
sharedrabundfloatvector.cpp
sharedrabundfloatvector.h
sharedrabundvector.cpp
sharedrabundvector.h
sharedsabundvector.cpp
sharedsabundvector.h
sharedsobs.cpp
sharedsobs.h
sharedsobscollectsummary.cpp
sharedsobscollectsummary.h
sharedsorabund.cpp
sharedsorabund.h
sharedsorclass.cpp
sharedsorclass.h
sharedsorest.cpp
sharedsorest.h
sharedthetan.cpp
sharedthetan.h
sharedthetayc.cpp
sharedthetayc.h
sharedutilities.cpp
sharedutilities.h
shen.cpp
shen.h
shhhercommand.cpp
shhhercommand.h
shhhseqscommand.cpp
shhhseqscommand.h
simpson.cpp
simpson.h
simpsoneven.cpp
simpsoneven.h
sinerp.f
singlelinkage.cpp
slayer.cpp
slayer.h
slibshuff.cpp
slibshuff.h
smithwilson.cpp
smithwilson.h
sobs.h
soergel.cpp
soergel.h
solow.cpp
solow.h
sortseqscommand.cpp
sortseqscommand.h
sparcccommand.cpp
sparcccommand.h
sparsedistancematrix.cpp
sparsedistancematrix.h
sparsematrix.cpp
sparsematrix.hpp
spearman.cpp
spearman.h
speciesprofile.cpp
speciesprofile.h
spline.cpp
spline.h
splitabundcommand.cpp
splitabundcommand.h
splitgroupscommand.cpp
splitgroupscommand.h
splitmatrix.cpp
splitmatrix.h
sslvrg.f
structchi2.cpp
structchi2.h
structchord.cpp
structchord.h
structeuclidean.cpp
structeuclidean.h
structkulczynski.cpp
structkulczynski.h
structpearson.cpp
structpearson.h
stxwx.f
subsample.cpp
subsample.h
subsamplecommand.cpp
subsamplecommand.h
suffixdb.cpp
suffixdb.hpp
suffixnodes.cpp
suffixnodes.hpp
suffixtree.cpp
suffixtree.hpp
summarycommand.cpp
summarycommand.h
summaryqualcommand.cpp
summaryqualcommand.h
summarysharedcommand.cpp
summarysharedcommand.h
summarytaxcommand.cpp
summarytaxcommand.h
systemcommand.cpp
systemcommand.h
taxonomyequalizer.cpp
taxonomyequalizer.h
taxonomynode.cpp
taxonomynode.h
tree.cpp
tree.h
treecalculator.h
treegroupscommand.cpp
treegroupscommand.h
treemap.cpp
treemap.h
treenode.cpp
treenode.h
treereader.cpp
treereader.h
trialSwap2.cpp
trialswap2.h
trimflowscommand.cpp
trimflowscommand.h
trimoligos.cpp
trimoligos.h
trimseqscommand.cpp
trimseqscommand.h
unifracunweightedcommand.cpp
unifracunweightedcommand.h
unifracweightedcommand.cpp
unifracweightedcommand.h
unweighted.cpp
unweighted.h
uvest.cpp
uvest.h
validcalculator.cpp
validcalculator.h
validparameter.cpp
validparameter.h
venn.cpp
venn.h
venncommand.cpp
venncommand.h
weighted.cpp
weighted.h
weightedlinkage.cpp
whittaker.cpp
whittaker.h