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Welcome to the mothur project, initiated by Dr. Patrick Schloss and his software development team in the Department of Microbiology & Immunology at The University of Michigan. This project seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community.
branch: master
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Mothur.xcodeproj added zapGremlins function to remove reoccurring bug with null charac…
uchime_src added uchime_src folder. added biom parameter to make.shared. added b…
.gitignore fixed issue with sffinfo and parse.fastq groups parse. added project.…
LICENSE adding license
Mothur.1 Changed back to xcode build.
abstractdecisiontree.cpp fixes while testing 1.33.0
abstractdecisiontree.hpp changes from april
abstractrandomforest.cpp finished dereplicate changes to chimera commands. added taxonomy file…
abstractrandomforest.hpp changes from april
ace.cpp Revert to previous commit
ace.h Revert to previous commit
aligncommand.cpp added oligos class. added check orient parameter to trim.flows, sffin…
aligncommand.h added zapGremlins function to remove reoccurring bug with null charac…
alignment.cpp added threshold parameter to make.contigs command.
alignment.hpp mods to resolve some misc warnings. added alignPrimer function to nee…
alignmentcell.cpp Revert to previous commit
alignmentcell.hpp Revert to previous commit
alignmentdb.cpp mods to resolve some misc warnings. added alignPrimer function to nee…
alignmentdb.h Revert to previous commit
alignnode.cpp changes from april
alignnode.h changes from april
aligntree.cpp changes from april
aligntree.h changes from april
amovacommand.cpp <= change for anova and homova. finished chimera.uchime dereplicate=t…
amovacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
anosimcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
anosimcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
averagelinkage.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i…
bayesian.cpp added make.lefse command. fixed bug in make.contigs with trimming rev…
bayesian.h added count file to get.groups and remove.groups. added shortcut para…
bellerophon.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
bellerophon.h Revert to previous commit
bergerparker.cpp Revert to previous commit
bergerparker.h Revert to previous commit
binsequencecommand.cpp adding labels to list file.
binsequencecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
blastalign.cpp Revert to previous commit
blastalign.hpp Revert to previous commit
blastdb.cpp added mothurgetpid function. fixed bug with align.seqs related to g++…
blastdb.hpp Revert to previous commit
boneh.cpp Revert to previous commit
boneh.h Revert to previous commit
bootstrap.cpp Revert to previous commit
bootstrap.h Revert to previous commit
bsplvb.f Revert to previous commit
bsplvd.f Revert to previous commit
bstick.cpp Revert to previous commit
bstick.h Revert to previous commit
bvalue.f Revert to previous commit
calcsparcc.cpp case sensitive include statement caused issues for Unix systems.
calcsparcc.h added sparcc command. fixed bug in remove.groups that removed all gro…
calculator.cpp Revert to previous commit
calculator.h added sharedotu parameter to venn command. working of make.contigs.
canberra.cpp Revert to previous commit
canberra.h Revert to previous commit
catchallcommand.cpp added get.dists and remove.dists commands. fixed bug in trim.seqs win…
catchallcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
ccode.cpp Revert to previous commit
ccode.h random stuff
chao1.cpp changes while testing
chao1.h Revert to previous commit
chimera.cpp Revert to previous commit
chimera.h working on dereplicate=t issue in chimera.slayer and chimera.perseus,…
chimerabellerophoncommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
chimerabellerophoncommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
chimeraccodecommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
chimeraccodecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
chimeracheckcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
chimeracheckcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
chimeracheckrdp.cpp Revert to previous commit
chimeracheckrdp.h random stuff
chimeraperseuscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
chimeraperseuscommand.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
chimerapintailcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
chimerapintailcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
chimerarealigner.cpp Revert to previous commit
chimerarealigner.h Revert to previous commit
chimeraslayer.cpp working on dereplicate=t issue in chimera.slayer and chimera.perseus,…
chimeraslayer.h working on dereplicate=t issue in chimera.slayer and chimera.perseus,…
chimeraslayercommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
chimeraslayercommand.h added zapGremlins function to remove reoccurring bug with null charac…
chimerauchimecommand.cpp fixed clearcut bug with distance out of range. fixed remove.seqs and …
chimerauchimecommand.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
chopseqscommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
chopseqscommand.h added zapGremlins function to remove reoccurring bug with null charac…
classify.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
classify.h added zap method to classify.seqs and changed bayesian method name to…
classifyotucommand.cpp added probabilities to "unclassified" in classify.otu. set processors…
classifyotucommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
classifyrfsharedcommand.cpp changes while testing
classifyrfsharedcommand.h changes while testing
classifyseqscommand.cpp removed couts and updated makefile
classifyseqscommand.h added zapGremlins function to remove reoccurring bug with null charac…
classifysvmsharedcommand.cpp fixing classifysvm conflicts
classifysvmsharedcommand.h fixing merge problem with classifysvmcommand.h
classifytreecommand.cpp added shared, constaxonomy and label parameter to get.lineage and rem…
classifytreecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
clearcut.cpp Revert to previous commit
clearcut.h Revert to previous commit
clearcutcommand.cpp fixed clearcut bug with distance out of range. fixed remove.seqs and …
clearcutcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
clearmemorycommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
clearmemorycommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
cluster.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i…
cluster.hpp make.lefse made OTU001 and OTU0001 equivalent to help with the list f…
clusterclassic.cpp paralellized chop.seqs
clusterclassic.h added count file to cluster.classic and cluster.split. modified split…
clustercommand.cpp adding labels to list file.
clustercommand.h random stuff
clusterdoturcommand.cpp adding labels to list file.
clusterdoturcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
clusterfragmentscommand.cpp cleaned up some warnings. worked on sra command.
clusterfragmentscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
clustersplitcommand.cpp fixed bug in mpi version of cluster.split. caused compile issue and h…
clustersplitcommand.h added file to cluster.split output. added warning to lefse code. fixe…
cmdargs.cpp Revert to previous commit
cmdargs.h Revert to previous commit
collect.cpp Revert to previous commit
collect.h Revert to previous commit
collectcommand.cpp added shannonrange calc.
collectcommand.h added shannonrange calc.
collectdisplay.h Revert to previous commit
collectorscurvedata.h Revert to previous commit
collectsharedcommand.cpp added rjsd calculator. improved work balance load between processors …
collectsharedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
command.hpp some minor typo
commandfactory.cpp added probabilities to "unclassified" in classify.otu. set processors…
commandfactory.hpp added mergesfffiles command. added current directories to get.current…
commandoptionparser.cpp added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v…
commandoptionparser.hpp Revert to previous commit
commandparameter.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
common.h Revert to previous commit
communitytype.cpp working on get.communitytype command
communitytype.h working on get.communitytype command
completelinkage.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i…
consensus.cpp cleaned up some warnings. worked on sra command.
consensus.h Revert to previous commit
consensusseqscommand.cpp adding labels to list file.
consensusseqscommand.h added mothurgetpid function. fixed bug with align.seqs related to g++…
cooccurrencecommand.cpp Merge remote-tracking branch 'origin/master'
cooccurrencecommand.h added binary file operations to mothurout class. added comment to seq…
corraxescommand.cpp adding labels to list file.
corraxescommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
countgroupscommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
countgroupscommand.h added *.count.summary file to count.groups command. added deltaq and …
countseqscommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
countseqscommand.h added zapGremlins function to remove reoccurring bug with null charac…
counttable.cpp counttable: Avoid adding extra whitespace at end of lines
counttable.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
coverage.cpp Revert to previous commit
coverage.h Revert to previous commit
createdatabasecommand.cpp added mothurgetpid function. fixed bug with align.seqs related to g++…
createdatabasecommand.h added count file to create.database command. corrected for change to …
currentfile.h Revert to previous commit
database.cpp Revert to previous commit
database.hpp Revert to previous commit
datavector.hpp adding labels to list file.
daxpy.f Revert to previous commit
dayhoff.h Revert to previous commit
ddot.f Revert to previous commit
decalc.cpp Revert to previous commit
decalc.h random stuff
decisiontree.cpp citation changes for 1.31.0
decisiontree.hpp changes from april
deconvolutecommand.cpp added mothurgetpid function. fixed bug with align.seqs related to g++…
deconvolutecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
degapseqscommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
degapseqscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
designmap.cpp added kruskal.wallis command. added worked on make.lefse. working of …
designmap.h added kruskal.wallis command. added worked on make.lefse. working of …
deuniqueseqscommand.cpp added mergesfffiles command. added current directories to get.current…
deuniqueseqscommand.h added binary file operations to mothurout class. added comment to seq…
deuniquetreecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
deuniquetreecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
display.h Revert to previous commit
dist.h Revert to previous commit
distancecommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
distancecommand.h added mothurOutJustToScreen function and changed all counter outputs …
distancedb.cpp Revert to previous commit
distancedb.hpp Revert to previous commit
distclearcut.cpp Revert to previous commit
distclearcut.h Revert to previous commit
dlibshuff.cpp Revert to previous commit
dlibshuff.h Revert to previous commit
dmat.cpp added zapGremlins function to remove reoccurring bug with null charac…
dmat.h Revert to previous commit
dpbfa.f Revert to previous commit
dpbsl.f Revert to previous commit
eachgapdist.h Revert to previous commit
eachgapdistignorens.h Revert to previous commit
eachgapignore.h Revert to previous commit
efron.cpp Revert to previous commit
efron.h Revert to previous commit
endiannessmacros.h Revert to previous commit
engine.cpp added zapGremlins function to remove reoccurring bug with null charac…
engine.hpp added code to check path for uchime and catchall executables
fasta.cpp Revert to previous commit
fasta.h Revert to previous commit
fastamap.cpp Revert to previous commit
fastamap.h Revert to previous commit
fileoutput.cpp Revert to previous commit
fileoutput.h Revert to previous commit
filters.h added lefse command. added check for hard filter length. fixed bug in…
filterseqscommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
filterseqscommand.h added zapGremlins function to remove reoccurring bug with null charac…
filtersharedcommand.cpp adding labels to list file.
filtersharedcommand.h added rarepercent and keepties parameters to the filter.shared command.
flowdata.cpp added Jensen-Shannon calc. working on get.communitytype command. fixe…
flowdata.h fixed problem where order=B was not checking for the maximum homopoly…
forest.cpp a lot of new input parameters in rf module, implemented a pruning sys…
forest.h changes from april
formatcolumn.cpp added sets to amova and homova commands. added oligos to make.contigs…
formatcolumn.h added sets to amova and homova commands. added oligos to make.contigs…
formatmatrix.h added sets to amova and homova commands. added oligos to make.contigs…
formatphylip.cpp added sets to amova and homova commands. added oligos to make.contigs…
formatphylip.h added sets to amova and homova commands. added oligos to make.contigs…
fullmatrix.cpp Revert to previous commit
fullmatrix.h Revert to previous commit
geom.cpp Revert to previous commit
geom.h Revert to previous commit
getcommandinfocommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
getcommandinfocommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getcoremicrobiomecommand.cpp adding labels to list file.
getcoremicrobiomecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getcurrentcommand.cpp added mergesfffiles command. added current directories to get.current…
getcurrentcommand.h added mergesfffiles command. added current directories to get.current…
getdistscommand.cpp added get.dists and remove.dists commands. fixed bug in trim.seqs win…
getdistscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win…
getgroupcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
getgroupcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getgroupscommand.cpp adding labels to list file.
getgroupscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getlabelcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
getlabelcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getlineagecommand.cpp fixed jest calc to return only value between 0 and 1. Modified reads …
getlineagecommand.h added shared, constaxonomy and label parameter to get.lineage and rem…
getlistcountcommand.cpp adding labels to list file.
getlistcountcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getmetacommunitycommand.cpp added probabilities to "unclassified" in classify.otu. set processors…
getmetacommunitycommand.h added rjsd calculator. improved work balance load between processors …
getmimarkspackagecommand.cpp worked on make.sra and get.mimarkspackage command. removed preprocess…
getmimarkspackagecommand.h added keytrim parameter to the merge.sfffiles command. working on mak…
getopt_long.cpp Revert to previous commit
getopt_long.h Revert to previous commit
getotulabelscommand.cpp modifications to commands to add headers to list file.
getotulabelscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win…
getoturepcommand.cpp added Jensen-Shannon calc. working on get.communitytype command. fixe…
getoturepcommand.h added binary file operations to mothurout class. added comment to seq…
getotuscommand.cpp adding labels to list file.
getotuscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getrabundcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
getrabundcommand.h added count file to get.sabund and get.rabund commands. fixed bug in …
getrelabundcommand.cpp adding labels to list file.
getrelabundcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
getsabundcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
getsabundcommand.h added count file to get.sabund and get.rabund commands. fixed bug in …
getseqscommand.cpp fixed clearcut bug with distance out of range. fixed remove.seqs and …
getseqscommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v…
getsharedotucommand.cpp fixes while testing 1.33.0
getsharedotucommand.h working on chimera.uchime change for dereplicate=t bug. added shared …
goodscoverage.cpp Revert to previous commit
goodscoverage.h Revert to previous commit
gotohoverlap.cpp Revert to previous commit
gotohoverlap.hpp Revert to previous commit
gower.cpp Revert to previous commit
gower.h Revert to previous commit
groupmap.cpp added rename.seqs command.
groupmap.h added rename.seqs command.
hamming.cpp Revert to previous commit
hamming.h Revert to previous commit
hcluster.cpp changes while testing 1.27
hcluster.h Revert to previous commit
hclustercommand.cpp adding labels to list file.
hclustercommand.h random stuff
heatmap.cpp pcr.seqs bug fix. working on shannon range calc
heatmap.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
heatmapcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
heatmapcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
heatmapsim.cpp Revert to previous commit
heatmapsim.h Revert to previous commit
heatmapsimcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
heatmapsimcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
heip.cpp Revert to previous commit
heip.h Revert to previous commit
hellinger.cpp Revert to previous commit
hellinger.h Revert to previous commit
helpcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
helpcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
homovacommand.cpp <= change for anova and homova. finished chimera.uchime dereplicate=t…
homovacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
ignoregaps.h Revert to previous commit
indicatorcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
indicatorcommand.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato…
inputdata.cpp fixes while testing 1.33.0
inputdata.h Revert to previous commit
interv.f Revert to previous commit
intrv.f Revert to previous commit
invsimpson.cpp Revert to previous commit
invsimpson.h Revert to previous commit
jackknife.cpp Revert to previous commit
jackknife.h Revert to previous commit
kmeans.cpp working on get.communitytype command
kmeans.h working on get.communitytype command
kmer.cpp Revert to previous commit
kmer.hpp Revert to previous commit
kmerdb.cpp Revert to previous commit
kmerdb.hpp Revert to previous commit
kmernode.cpp changes from april
kmernode.h changes from april
kmertree.cpp changes from april
kmertree.h changes from april
knn.cpp added count file to get.groups and remove.groups. added shortcut para…
knn.h Revert to previous commit
kruskalwalliscommand.cpp adding labels to list file.
kruskalwalliscommand.h changes while testing
lefsecommand.cpp added file to cluster.split output. added warning to lefse code. fixe…
lefsecommand.h changes while testing
libshuff.cpp Revert to previous commit
libshuff.h mods to resolve some misc warnings. added alignPrimer function to nee…
libshuffcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
libshuffcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
linearalgebra.cpp fixed jest calc to return only value between 0 and 1. Modified reads …
linearalgebra.h added Jensen-Shannon calc. working on get.communitytype command. fixe…
listotulabelscommand.cpp adding labels to list file.
listotulabelscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win…
listseqscommand.cpp added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v…
listseqscommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v…
listvector.cpp added zapGremlins function to remove reoccurring bug with null charac…
listvector.hpp adding labels to list file.
loadlogfilecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
loadlogfilecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
logsd.cpp Revert to previous commit
logsd.h Revert to previous commit
macros.h changes from april
makebiomcommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
makebiomcommand.h added zapGremlins function to remove reoccurring bug with null charac…
makecontigscommand.cpp worked on make.sra and get.mimarkspackage command. removed preprocess…
makecontigscommand.h worked on make.sra and get.mimarkspackage command. removed preprocess…
makefastqcommand.cpp added *.count.summary file to count.groups command. added deltaq and …
makefastqcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
makefile removed couts and updated makefile
makegroupcommand.cpp added file to cluster.split output. added warning to lefse code. fixe…
makegroupcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
makelefsecommand.cpp make.lefse made OTU001 and OTU0001 equivalent to help with the list f…
makelefsecommand.h make.lefse made OTU001 and OTU0001 equivalent to help with the list f…
makelookupcommand.cpp changes while testing
makelookupcommand.h citation changes for 1.31.0
maligner.cpp Revert to previous commit
maligner.h Revert to previous commit
manhattan.cpp Revert to previous commit
manhattan.h Revert to previous commit
mantelcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
mantelcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
matrixoutputcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
matrixoutputcommand.h added rjsd calculator. improved work balance load between processors …
memchi2.cpp Revert to previous commit
memchi2.h Revert to previous commit
memchord.cpp Revert to previous commit
memchord.h Revert to previous commit
memeuclidean.cpp Revert to previous commit
memeuclidean.h Revert to previous commit
mempearson.cpp Revert to previous commit
mempearson.h Revert to previous commit
mergefilecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
mergefilecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
mergegroupscommand.cpp adding labels to list file.
mergegroupscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
mergesfffilecommand.cpp added keytrim parameter to the merge.sfffiles command. working on mak…
mergesfffilecommand.h added keytrim parameter to the merge.sfffiles command. working on mak…
mergetaxsummarycommand.cpp added more output to fasta files about diffs in make.contigs and trim…
mergetaxsummarycommand.h added merge.taxsummary command. added column format to dist.shared.
metastatscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
metastatscommand.h changed name of get.metacommunity to get.communitytype. fixed bug in …
mgclustercommand.cpp adding labels to list file.
mgclustercommand.h Update mgcluster to use dist=1 for missing distances when no cutoff i…
mothur.cpp fixed issue in svm.hpp that caused compile problem with 32 bit. "moth…
mothur.h make.lefse made OTU001 and OTU0001 equivalent to help with the list f…
mothurfisher.cpp Revert to previous commit
mothurfisher.h Revert to previous commit
mothurmetastats.cpp adding labels to list file.
mothurmetastats.h changed name of get.metacommunity to get.communitytype. fixed bug in …
mothurout.cpp added keytrim parameter to the merge.sfffiles command. working on mak…
mothurout.h fixed sffinfo bug
myPerseus.cpp Revert to previous commit
myPerseus.h Revert to previous commit
myseqdist.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
myseqdist.h Revert to previous commit
nameassignment.cpp changes from april
nameassignment.hpp fixed subsample name file name issue. added count parameter to cluste…
nast.cpp Revert to previous commit
nast.hpp Revert to previous commit
nastreport.cpp Revert to previous commit
nastreport.hpp Revert to previous commit
needlemanoverlap.cpp added adjustDots function to pcr.seqs, keeps sequences aligned in cas…
needlemanoverlap.hpp mods to resolve some misc warnings. added alignPrimer function to nee…
newcommandtemplate.cpp Test new machine.
newcommandtemplate.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
nmdscommand.cpp added binary file operations to mothurout class. added comment to seq…
nmdscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
noalign.cpp Revert to previous commit
noalign.hpp Revert to previous commit
nocommands.cpp Revert to previous commit
nocommands.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
normalizesharedcommand.cpp adding labels to list file.
normalizesharedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
npshannon.cpp Revert to previous commit
npshannon.h Revert to previous commit
nseqs.h Revert to previous commit
observable.h Revert to previous commit
odum.cpp Revert to previous commit
odum.h Revert to previous commit
oligos.cpp added keytrim parameter to the merge.sfffiles command. working on mak…
oligos.h added oligos class. added check orient parameter to trim.flows, sffin…
onegapdist.h Revert to previous commit
onegapignore.h Revert to previous commit
optionparser.cpp added method parameter to get.oturep. options method=abundance or dis…
optionparser.h added load.logfile command. changed summary.single output for subsamp…
ordervector.cpp Revert to previous commit
ordervector.hpp Revert to previous commit
otuassociationcommand.cpp adding labels to list file.
otuassociationcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
otuhierarchycommand.cpp fixes while testing 1.33.0
otuhierarchycommand.h fixes while testing 1.33.0
overlap.cpp Revert to previous commit
overlap.hpp Revert to previous commit
pairwiseseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
pairwiseseqscommand.h added lefse command. added check for hard filter length. fixed bug in…
pam.cpp fixes while building
pam.h added mergesfffiles command. added current directories to get.current…
parsefastaqcommand.cpp added keytrim parameter to the merge.sfffiles command. working on mak…
parsefastaqcommand.h added keytrim parameter to the merge.sfffiles command. working on mak…
parselistscommand.cpp modifications to commands to add headers to list file.
parselistscommand.h modifications to commands to add headers to list file.
parsimony.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
parsimony.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato…
parsimonycommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
parsimonycommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
pcacommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
pcacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
pcoacommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
pcoacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
pcrseqscommand.h added keytrim parameter to the merge.sfffiles command. working on mak…
phylodiversitycommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
phylodiversitycommand.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato…
phylosummary.cpp added relabund parameter to classify.seqs and summary.tax commands
phylosummary.h added relabund parameter to classify.seqs and summary.tax commands
phylotree.cpp added picrust and ref taxonomy parameters to make.biom
phylotree.h added picrust and ref taxonomy parameters to make.biom
phylotypecommand.cpp fixing classifysvm conflicts
phylotypecommand.h added end of file character to some type type reads. fixes while test…
pintail.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
pintail.h random stuff
pipelinepdscommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
pipelinepdscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
prcseqscommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
preclustercommand.cpp changes from april
preclustercommand.h added mothurOutJustToScreen function and changed all counter outputs …
primerdesigncommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
primerdesigncommand.h modifications to commands to add headers to list file.
prng.cpp Revert to previous commit
prng.h Revert to previous commit
progress.cpp Revert to previous commit
progress.hpp Revert to previous commit
qFinderDMM.cpp fixed jest calc to return only value between 0 and 1. Modified reads …
qFinderDMM.h added Jensen-Shannon calc. working on get.communitytype command. fixe…
qstat.cpp Revert to previous commit
qstat.h Revert to previous commit
qualityscores.cpp added oligos class. added check orient parameter to trim.flows, sffin…
qualityscores.h added oligos class. added check orient parameter to trim.flows, sffin…
quitcommand.cpp Revert to previous commit
quitcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
rabundvector.cpp added shannonrange calc.
rabundvector.hpp Revert to previous commit
randomforest.cpp adding labels to list file.
randomforest.hpp adding misclassification output file
randomnumber.cpp added sparcc command. fixed bug in remove.groups that removed all gro…
randomnumber.h added sparcc command. fixed bug in remove.groups that removed all gro…
rarecalc.cpp Revert to previous commit
rarecalc.h Revert to previous commit
raredisplay.cpp changed how rarefaction commands find the lci and hci. they now save …
raredisplay.h changed how rarefaction commands find the lci and hci. they now save …
rarefact.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
rarefact.h forced rarefaction.single to output ending line for all groups. added…
rarefactcommand.cpp added mothurgetpid function. fixed bug with align.seqs related to g++…
rarefactcommand.h added shannonrange calc.
rarefactioncurvedata.h Revert to previous commit
rarefactsharedcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
rarefactsharedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
readblast.cpp added warning to readBlast to warn about duplicate names in the blast…
readblast.h fixed outputName creator, added debugging to readblast
readcluster.cpp added SequenceCountParser class to parse the count table by group. ad…
readcluster.h added SequenceCountParser class to parse the count table by group. ad…
readcolumn.cpp paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato…
readcolumn.h fixed subsample name file name issue. added count parameter to cluste…
readmatrix.hpp changes while testing 1.27
readphylip.cpp fixed subsample name file name issue. added count parameter to cluste…
readphylip.h fixed subsample name file name issue. added count parameter to cluste…
readphylipvector.cpp Revert to previous commit
readphylipvector.h Revert to previous commit
readtree.cpp added name, group and count files to chop.seqs. added intelligent war…
readtree.h major change to the tree class to use the count table class instead o…
refchimeratest.cpp fixed seq. error align=f issue. added std and ave calcs to mothurout.…
refchimeratest.h Changes to seq.error so that an alignment is not necessary
referencedb.cpp Revert to previous commit
referencedb.h Revert to previous commit
regularizeddecisiontree.cpp added files for regularized random forest
regularizeddecisiontree.h added files for regularized random forest
regularizedrandomforest.cpp a lot of new input parameters in rf module, implemented a pruning sys…
regularizedrandomforest.h added files for regularized random forest
removedistscommand.cpp added get.dists and remove.dists commands. fixed bug in trim.seqs win…
removedistscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win…
removegroupscommand.cpp modifications to commands to add headers to list file.
removegroupscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
removelineagecommand.cpp fixed jest calc to return only value between 0 and 1. Modified reads …
removelineagecommand.h added shared, constaxonomy and label parameter to get.lineage and rem…
removeotulabelscommand.cpp modifications to commands to add headers to list file.
removeotulabelscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win…
removeotuscommand.cpp modifications to commands to add headers to list file.
removeotuscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
removerarecommand.cpp modifications to commands to add headers to list file.
removerarecommand.h added count file to get.sabund and get.rabund commands. fixed bug in …
removeseqscommand.cpp fixed clearcut bug with distance out of range. fixed remove.seqs and …
removeseqscommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v…
renameseqscommand.cpp changes while testing
renameseqscommand.h added rename.seqs command.
reportfile.cpp Revert to previous commit
reportfile.h Revert to previous commit
reversecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
reversecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
rftreenode.cpp a lot of new input parameters in rf module, implemented a pruning sys…
rftreenode.hpp changes from april
sabundvector.cpp added shannonrange calc.
sabundvector.hpp Revert to previous commit
screenseqscommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
screenseqscommand.h added zapGremlins function to remove reoccurring bug with null charac…
secondarystructurecommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
secondarystructurecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
sensspeccommand.cpp modifications to commands to add headers to list file.
sensspeccommand.h added square format for phylipfile. made command work with list files…
seqerrorcommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
seqerrorcommand.h working on dereplicate=t issue in chimera.slayer and chimera.perseus,…
seqnoise.cpp modifications to commands to add headers to list file.
seqnoise.h Revert to previous commit
seqsummarycommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
seqsummarycommand.h added zapGremlins function to remove reoccurring bug with null charac…
sequence.cpp added probabilities to "unclassified" in classify.otu. set processors…
sequence.hpp added probabilities to "unclassified" in classify.otu. set processors…
sequencecountparser.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
sequencecountparser.h added SequenceCountParser class to parse the count table by group. ad…
sequencedb.cpp Revert to previous commit
sequencedb.h Revert to previous commit
sequenceparser.cpp added count file to chimera.uchime. found issue with uchime program t…
sequenceparser.h added SequenceCountParser class to parse the count table by group. ad…
setcurrentcommand.cpp added binary file operations to mothurout class. added comment to seq…
setcurrentcommand.h added method parameter to get.oturep. options method=abundance or dis…
setdircommand.cpp added make.lefse command. fixed bug in make.contigs with trimming rev…
setdircommand.h added modify names parameter to set.dir
setlogfilecommand.cpp changes while testing
setlogfilecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
sffinfocommand.cpp added keytrim parameter to the merge.sfffiles command. working on mak…
sffinfocommand.h added probabilities to "unclassified" in classify.otu. set processors…
sffmultiplecommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
sffmultiplecommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v…
sgram.f Revert to previous commit
shannon.cpp Revert to previous commit
shannon.h Revert to previous commit
shannoneven.cpp Revert to previous commit
shannoneven.h Revert to previous commit
shannonrange.cpp added shared file to make.table
shannonrange.h added shannonrange calc.
sharedace.cpp Revert to previous commit
sharedace.h Revert to previous commit
sharedanderbergs.cpp Revert to previous commit
sharedanderbergs.h Revert to previous commit
sharedbraycurtis.cpp Revert to previous commit
sharedbraycurtis.h Revert to previous commit
sharedchao1.cpp Revert to previous commit
sharedchao1.h Revert to previous commit
sharedcommand.cpp added file to cluster.split output. added warning to lefse code. fixe…
sharedcommand.h added file to cluster.split output. added warning to lefse code. fixe…
sharedjabund.cpp Revert to previous commit
sharedjabund.h Revert to previous commit
sharedjackknife.cpp Revert to previous commit
sharedjackknife.h Revert to previous commit
sharedjclass.cpp Revert to previous commit
sharedjclass.h Revert to previous commit
sharedjest.cpp fixed jest calc to return only value between 0 and 1. Modified reads …
sharedjest.h Revert to previous commit
sharedjsd.cpp converted jsd calculation to be based on relative abundance
sharedjsd.h added Jensen-Shannon calc. working on get.communitytype command. fixe…
sharedkstest.cpp Revert to previous commit
sharedkstest.h Revert to previous commit
sharedkulczynski.cpp Revert to previous commit
sharedkulczynski.h Revert to previous commit
sharedkulczynskicody.cpp Revert to previous commit
sharedkulczynskicody.h Revert to previous commit
sharedlennon.cpp Revert to previous commit
sharedlennon.h Revert to previous commit
sharedlistvector.cpp adding labels to list file.
sharedlistvector.h adding labels to list file.
sharedmarczewski.cpp Revert to previous commit
sharedmarczewski.h Revert to previous commit
sharedmorisitahorn.cpp Revert to previous commit
sharedmorisitahorn.h Revert to previous commit
sharednseqs.h Revert to previous commit
sharedochiai.cpp Revert to previous commit
sharedochiai.h Revert to previous commit
sharedordervector.cpp adding labels to list file.
sharedordervector.h Revert to previous commit
sharedrabundfloatvector.cpp adding labels to list file.
sharedrabundfloatvector.h added sparcc command. fixed bug in remove.groups that removed all gro…
sharedrabundvector.cpp adding labels to list file.
sharedrabundvector.h added get.metacommunity command.
sharedrjsd.cpp added rjsd calculator. improved work balance load between processors …
sharedrjsd.h added rjsd calculator. improved work balance load between processors …
sharedsabundvector.cpp Revert to previous commit
sharedsabundvector.h Revert to previous commit
sharedsobs.cpp Revert to previous commit
sharedsobs.h Revert to previous commit
sharedsobscollectsummary.cpp adding labels to list file.
sharedsobscollectsummary.h added sharedotu parameter to venn command. working of make.contigs.
sharedsorabund.cpp Revert to previous commit
sharedsorabund.h Revert to previous commit
sharedsorclass.cpp Revert to previous commit
sharedsorclass.h Revert to previous commit
sharedsorest.cpp Revert to previous commit
sharedsorest.h Revert to previous commit
sharedthetan.cpp Revert to previous commit
sharedthetan.h Revert to previous commit
sharedthetayc.cpp added filter.shared command. fixed lci and uci for thetayc calc
sharedthetayc.h Revert to previous commit
sharedutilities.cpp fixed issue in tree.shared when shared file was not sorted
sharedutilities.h Revert to previous commit
shen.cpp Revert to previous commit
shen.h Revert to previous commit
shhhercommand.cpp fixed bug in mpi version of cluster.split. caused compile issue and h…
shhhercommand.h added order=A or order=B to trim.flows and shhh.flows commands. added…
shhhseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
shhhseqscommand.h added checks to make sure windows processes completed their tasks.
simpson.cpp Revert to previous commit
simpson.h Revert to previous commit
simpsoneven.cpp Revert to previous commit
simpsoneven.h Revert to previous commit
sinerp.f Revert to previous commit
singlelinkage.cpp make.lefse made OTU001 and OTU0001 equivalent to help with the list f…
slayer.cpp Revert to previous commit
slayer.h Revert to previous commit
slibshuff.cpp Revert to previous commit
slibshuff.h Revert to previous commit
smithwilson.cpp Revert to previous commit
smithwilson.h Revert to previous commit
sobs.h Revert to previous commit
soergel.cpp Revert to previous commit
soergel.h Revert to previous commit
solow.cpp Revert to previous commit
solow.h Revert to previous commit
sortseqscommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
sortseqscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
sparcccommand.cpp mods while testing
sparcccommand.h citation changes for 1.31.0
sparsedistancematrix.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i…
sparsedistancematrix.h Update mgcluster to use dist=1 for missing distances when no cutoff i…
sparsematrix.cpp Revert to previous commit
sparsematrix.hpp Revert to previous commit
spearman.cpp Revert to previous commit
spearman.h Revert to previous commit
speciesprofile.cpp Revert to previous commit
speciesprofile.h Revert to previous commit
spline.cpp Revert to previous commit
spline.h Revert to previous commit
splitabundcommand.cpp modifications to commands to add headers to list file.
splitabundcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
splitgroupscommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
splitgroupscommand.h added topdown parameter to pre.cluster. added more debugging output t…
splitmatrix.cpp Merge pull request #5 from jonls/splitmatrix-no-reopen
splitmatrix.h fixed bug in mpi version of cluster.split. caused compile issue and h…
sracommand.cpp worked on make.sra and get.mimarkspackage command. removed preprocess…
sracommand.h added keytrim parameter to the merge.sfffiles command. working on mak…
sslvrg.f Revert to previous commit
structchi2.cpp Revert to previous commit
structchi2.h Revert to previous commit
structchord.cpp Revert to previous commit
structchord.h Revert to previous commit
structeuclidean.cpp Revert to previous commit
structeuclidean.h Revert to previous commit
structkulczynski.cpp Revert to previous commit
structkulczynski.h Revert to previous commit
structpearson.cpp Revert to previous commit
structpearson.h Revert to previous commit
stxwx.f Revert to previous commit
subsample.cpp adding labels to list file.
subsample.h added classify.shared command and random forest files. added count fi…
subsamplecommand.cpp cleaned up some warnings. worked on sra command.
subsamplecommand.h modifications to commands to add headers to list file.
suffixdb.cpp Revert to previous commit
suffixdb.hpp Revert to previous commit
suffixnodes.cpp Revert to previous commit
suffixnodes.hpp Revert to previous commit
suffixtree.cpp Revert to previous commit
suffixtree.hpp Revert to previous commit
summarycommand.cpp added shannonrange calc.
summarycommand.h added shannonrange calc.
summaryqualcommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
summaryqualcommand.h added zapGremlins function to remove reoccurring bug with null charac…
summarysharedcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
summarysharedcommand.h added rjsd calculator. improved work balance load between processors …
summarytaxcommand.cpp added relabund parameter to classify.seqs and summary.tax commands
summarytaxcommand.h added relabund parameter to classify.seqs and summary.tax commands
svm.cpp fixing classifysvm conflicts
svm.hpp fixed issue in svm.hpp that caused compile problem with 32 bit. "moth…
systemcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre…
systemcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
taxonomyequalizer.cpp Revert to previous commit
taxonomyequalizer.h Revert to previous commit
taxonomynode.cpp changes from april
taxonomynode.h changes from april
tree.cpp added name, group and count files to chop.seqs. added intelligent war…
tree.h added name, group and count files to chop.seqs. added intelligent war…
treecalculator.h Revert to previous commit
treegroupscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
treegroupscommand.h tree.shared windows processors > 2 fixes while testing.
treemap.cpp added count file to get.oturep, pre.cluster, screen.seqs, tree.shared…
treemap.h major change to the tree class to use the count table class instead o…
treenode.cpp Revert to previous commit
treenode.h Revert to previous commit
treereader.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and…
treereader.h major change to the tree class to use the count table class instead o…
trialSwap2.cpp mods to resolve some misc warnings. added alignPrimer function to nee…
trialswap2.h added functions to calculate standard deviation and zscore
trimflowscommand.cpp added more output to fasta files about diffs in make.contigs and trim…
trimflowscommand.h added pdiffs to reverse primers.
trimoligos.cpp added zapGremlins function to remove reoccurring bug with null charac…
trimoligos.h added zapGremlins function to remove reoccurring bug with null charac…
trimseqscommand.cpp added zapGremlins function to remove reoccurring bug with null charac…
trimseqscommand.h added more output to fasta files about diffs in make.contigs and trim…
unifracunweightedcommand.cpp added lefse command. added check for hard filter length. fixed bug in…
unifracunweightedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre…
unifracweightedcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
unifracweightedcommand.h added lefse command. added check for hard filter length. fixed bug in…
unweighted.cpp cleaned up some warnings. worked on sra command.
unweighted.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato…
uvest.cpp Revert to previous commit
uvest.h Revert to previous commit
validcalculator.cpp added mothurgetpid function. fixed bug with align.seqs related to g++…
validcalculator.h Revert to previous commit
validparameter.cpp worked on make.sra and get.mimarkspackage command. removed preprocess…
validparameter.h Revert to previous commit
venn.cpp added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v…
venn.h added sharedotu parameter to venn command. working of make.contigs.
venncommand.cpp fixes while testing 1.33.0
venncommand.h added binary file operations to mothurout class. added comment to seq…
weighted.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand.
weighted.h paralellized unifrac.weighted for windows. added get.metacommunity co…
weightedlinkage.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i…
whittaker.cpp Revert to previous commit
whittaker.h Revert to previous commit
wilcox.cpp changed name of get.metacommunity to get.communitytype. fixed bug in …
wilcox.h changed name of get.metacommunity to get.communitytype. fixed bug in …
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