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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
Octocat-spinner-32 Mothur.xcodeproj added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 uchime_src added uchime_src folder. added biom parameter to make.shared. added b… April 20, 2012
Octocat-spinner-32 .gitignore asdf July 17, 2013
Octocat-spinner-32 LICENSE adding license February 07, 2011
Octocat-spinner-32 Mothur.1 Changed back to xcode build. January 04, 2011
Octocat-spinner-32 abstractdecisiontree.cpp fixes while testing 1.33.0 February 10, 2014
Octocat-spinner-32 abstractdecisiontree.hpp fixes while testing 1.33.0 February 10, 2014
Octocat-spinner-32 abstractrandomforest.cpp finished dereplicate changes to chimera commands. added taxonomy file… March 19, 2013
Octocat-spinner-32 abstractrandomforest.hpp added classify.shared command and random forest files. added count fi… October 02, 2012
Octocat-spinner-32 ace.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 ace.h Revert to previous commit May 02, 2012
Octocat-spinner-32 aligncommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 aligncommand.h added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 alignment.cpp added threshold parameter to make.contigs command. May 18, 2012
Octocat-spinner-32 alignment.hpp mods to resolve some misc warnings. added alignPrimer function to nee… February 27, 2013
Octocat-spinner-32 alignmentcell.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 alignmentcell.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 alignmentdb.cpp mods to resolve some misc warnings. added alignPrimer function to nee… February 27, 2013
Octocat-spinner-32 alignmentdb.h Revert to previous commit May 02, 2012
Octocat-spinner-32 alignnode.cpp added sets to amova and homova commands. added oligos to make.contigs… October 22, 2012
Octocat-spinner-32 alignnode.h added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 aligntree.cpp added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 aligntree.h added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 amovacommand.cpp <= change for anova and homova. finished chimera.uchime dereplicate=t… March 06, 2013
Octocat-spinner-32 amovacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 anosimcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 anosimcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 averagelinkage.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 bayesian.cpp added make.lefse command. fixed bug in make.contigs with trimming rev… June 13, 2013
Octocat-spinner-32 bayesian.h added count file to get.groups and remove.groups. added shortcut para… September 11, 2012
Octocat-spinner-32 bellerophon.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 bellerophon.h Revert to previous commit May 02, 2012
Octocat-spinner-32 bergerparker.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 bergerparker.h Revert to previous commit May 02, 2012
Octocat-spinner-32 binsequencecommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 binsequencecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 blastalign.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 blastalign.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 blastdb.cpp added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 blastdb.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 boneh.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 boneh.h Revert to previous commit May 02, 2012
Octocat-spinner-32 bootstrap.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 bootstrap.h Revert to previous commit May 02, 2012
Octocat-spinner-32 bsplvb.f Revert to previous commit May 02, 2012
Octocat-spinner-32 bsplvd.f Revert to previous commit May 02, 2012
Octocat-spinner-32 bstick.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 bstick.h Revert to previous commit May 02, 2012
Octocat-spinner-32 bvalue.f Revert to previous commit May 02, 2012
Octocat-spinner-32 calcsparcc.cpp case sensitive include statement caused issues for Unix systems. May 28, 2013
Octocat-spinner-32 calcsparcc.h added sparcc command. fixed bug in remove.groups that removed all gro… May 13, 2013
Octocat-spinner-32 calculator.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 calculator.h added sharedotu parameter to venn command. working of make.contigs. December 18, 2012
Octocat-spinner-32 canberra.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 canberra.h Revert to previous commit May 02, 2012
Octocat-spinner-32 catchallcommand.cpp added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 catchallcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 ccode.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 ccode.h random stuff September 04, 2013
Octocat-spinner-32 chao1.cpp changes while testing October 02, 2013
Octocat-spinner-32 chao1.h Revert to previous commit May 02, 2012
Octocat-spinner-32 chimera.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 chimera.h working on dereplicate=t issue in chimera.slayer and chimera.perseus,… March 18, 2013
Octocat-spinner-32 chimerabellerophoncommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 chimerabellerophoncommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 chimeraccodecommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 chimeraccodecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 chimeracheckcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 chimeracheckcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 chimeracheckrdp.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 chimeracheckrdp.h random stuff September 04, 2013
Octocat-spinner-32 chimeraperseuscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 chimeraperseuscommand.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 chimerapintailcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 chimerapintailcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 chimerarealigner.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 chimerarealigner.h Revert to previous commit May 02, 2012
Octocat-spinner-32 chimeraslayer.cpp working on dereplicate=t issue in chimera.slayer and chimera.perseus,… March 18, 2013
Octocat-spinner-32 chimeraslayer.h working on dereplicate=t issue in chimera.slayer and chimera.perseus,… March 18, 2013
Octocat-spinner-32 chimeraslayercommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 chimeraslayercommand.h added mothurOutJustToScreen function and changed all counter outputs … April 19, 2013
Octocat-spinner-32 chimerauchimecommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 chimerauchimecommand.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 chopseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 chopseqscommand.h added name, group and count files to chop.seqs. added intelligent war… April 03, 2013
Octocat-spinner-32 classify.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 classify.h added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 classifyotucommand.cpp added relabund parameter to classify.seqs and summary.tax commands February 04, 2014
Octocat-spinner-32 classifyotucommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 classifyrfsharedcommand.cpp changes while testing October 02, 2013
Octocat-spinner-32 classifyrfsharedcommand.h changes while testing October 02, 2013
Octocat-spinner-32 classifyseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 classifyseqscommand.h added relabund parameter to classify.seqs and summary.tax commands February 04, 2014
Octocat-spinner-32 classifytreecommand.cpp added shared, constaxonomy and label parameter to get.lineage and rem… April 29, 2013
Octocat-spinner-32 classifytreecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 clearcut.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 clearcut.h Revert to previous commit May 02, 2012
Octocat-spinner-32 clearcutcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 clearcutcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 clearmemorycommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 clearmemorycommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 cluster.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 cluster.hpp Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 clusterclassic.cpp paralellized chop.seqs August 01, 2012
Octocat-spinner-32 clusterclassic.h added count file to cluster.classic and cluster.split. modified split… July 31, 2012
Octocat-spinner-32 clustercommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 clustercommand.h random stuff September 04, 2013
Octocat-spinner-32 clusterdoturcommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 clusterdoturcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 clusterfragmentscommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 clusterfragmentscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 clustersplitcommand.cpp working on sra and get.mimarkspackage commands. added file parameter … April 02, 2014
Octocat-spinner-32 clustersplitcommand.h working on sra and get.mimarkspackage commands. added file parameter … April 02, 2014
Octocat-spinner-32 cmdargs.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 cmdargs.h Revert to previous commit May 02, 2012
Octocat-spinner-32 collect.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 collect.h Revert to previous commit May 02, 2012
Octocat-spinner-32 collectcommand.cpp added shannonrange calc. March 05, 2014
Octocat-spinner-32 collectcommand.h added shannonrange calc. March 05, 2014
Octocat-spinner-32 collectdisplay.h Revert to previous commit May 02, 2012
Octocat-spinner-32 collectorscurvedata.h Revert to previous commit May 02, 2012
Octocat-spinner-32 collectsharedcommand.cpp added rjsd calculator. improved work balance load between processors … January 21, 2014
Octocat-spinner-32 collectsharedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 command.hpp some minor typo February 07, 2013
Octocat-spinner-32 commandfactory.cpp working of get.mimarkspackage and sra command April 01, 2014
Octocat-spinner-32 commandfactory.hpp added mergesfffiles command. added current directories to get.current… February 03, 2014
Octocat-spinner-32 commandoptionparser.cpp added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v… October 17, 2013
Octocat-spinner-32 commandoptionparser.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 commandparameter.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 common.h Revert to previous commit May 02, 2012
Octocat-spinner-32 communitytype.cpp working on get.communitytype command January 29, 2014
Octocat-spinner-32 communitytype.h working on get.communitytype command January 29, 2014
Octocat-spinner-32 completelinkage.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 consensus.cpp major change to the tree class to use the count table class instead o… September 07, 2012
Octocat-spinner-32 consensus.h Revert to previous commit May 02, 2012
Octocat-spinner-32 consensusseqscommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 consensusseqscommand.h added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 cooccurrencecommand.cpp Merge remote-tracking branch 'origin/master' December 13, 2012
Octocat-spinner-32 cooccurrencecommand.h added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 corraxescommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 corraxescommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 countgroupscommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 countgroupscommand.h added *.count.summary file to count.groups command. added deltaq and … February 06, 2013
Octocat-spinner-32 countseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 countseqscommand.h added shared file to make.table March 06, 2014
Octocat-spinner-32 counttable.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 counttable.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 coverage.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 coverage.h Revert to previous commit May 02, 2012
Octocat-spinner-32 createdatabasecommand.cpp added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 createdatabasecommand.h added count file to create.database command. corrected for change to … May 14, 2013
Octocat-spinner-32 currentfile.h Revert to previous commit May 02, 2012
Octocat-spinner-32 database.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 database.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 datavector.hpp adding labels to list file. October 17, 2013
Octocat-spinner-32 daxpy.f Revert to previous commit May 02, 2012
Octocat-spinner-32 dayhoff.h Revert to previous commit May 02, 2012
Octocat-spinner-32 ddot.f Revert to previous commit May 02, 2012
Octocat-spinner-32 decalc.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 decalc.h random stuff September 04, 2013
Octocat-spinner-32 decisiontree.cpp citation changes for 1.31.0 May 28, 2013
Octocat-spinner-32 decisiontree.hpp a lot of new input parameters in rf module, implemented a pruning sys… May 02, 2013
Octocat-spinner-32 deconvolutecommand.cpp added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 deconvolutecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 degapseqscommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 degapseqscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 designmap.cpp added kruskal.wallis command. added worked on make.lefse. working of … June 24, 2013
Octocat-spinner-32 designmap.h added kruskal.wallis command. added worked on make.lefse. working of … June 24, 2013
Octocat-spinner-32 deuniqueseqscommand.cpp added mergesfffiles command. added current directories to get.current… February 03, 2014
Octocat-spinner-32 deuniqueseqscommand.h added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 deuniquetreecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 deuniquetreecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 display.h Revert to previous commit May 02, 2012
Octocat-spinner-32 dist.h Revert to previous commit May 02, 2012
Octocat-spinner-32 distancecommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 distancecommand.h added mothurOutJustToScreen function and changed all counter outputs … April 19, 2013
Octocat-spinner-32 distancedb.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 distancedb.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 distclearcut.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 distclearcut.h Revert to previous commit May 02, 2012
Octocat-spinner-32 dlibshuff.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 dlibshuff.h Revert to previous commit May 02, 2012
Octocat-spinner-32 dmat.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 dmat.h Revert to previous commit May 02, 2012
Octocat-spinner-32 dpbfa.f Revert to previous commit May 02, 2012
Octocat-spinner-32 dpbsl.f Revert to previous commit May 02, 2012
Octocat-spinner-32 eachgapdist.h Revert to previous commit May 02, 2012
Octocat-spinner-32 eachgapdistignorens.h Revert to previous commit May 02, 2012
Octocat-spinner-32 eachgapignore.h Revert to previous commit May 02, 2012
Octocat-spinner-32 efron.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 efron.h Revert to previous commit May 02, 2012
Octocat-spinner-32 endiannessmacros.h Revert to previous commit May 02, 2012
Octocat-spinner-32 engine.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 engine.hpp added code to check path for uchime and catchall executables May 29, 2012
Octocat-spinner-32 fasta.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 fasta.h Revert to previous commit May 02, 2012
Octocat-spinner-32 fastamap.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 fastamap.h Revert to previous commit May 02, 2012
Octocat-spinner-32 fileoutput.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 fileoutput.h Revert to previous commit May 02, 2012
Octocat-spinner-32 filters.h added lefse command. added check for hard filter length. fixed bug in… September 18, 2013
Octocat-spinner-32 filterseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 filterseqscommand.h added mothurOutJustToScreen function and changed all counter outputs … April 19, 2013
Octocat-spinner-32 filtersharedcommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 filtersharedcommand.h added rarepercent and keepties parameters to the filter.shared command. April 08, 2013
Octocat-spinner-32 flowdata.cpp added Jensen-Shannon calc. working on get.communitytype command. fixe… January 09, 2014
Octocat-spinner-32 flowdata.h fixed problem where order=B was not checking for the maximum homopoly… July 17, 2013
Octocat-spinner-32 forest.cpp a lot of new input parameters in rf module, implemented a pruning sys… May 02, 2013
Octocat-spinner-32 forest.h a lot of new input parameters in rf module, implemented a pruning sys… May 02, 2013
Octocat-spinner-32 formatcolumn.cpp added sets to amova and homova commands. added oligos to make.contigs… October 22, 2012
Octocat-spinner-32 formatcolumn.h added sets to amova and homova commands. added oligos to make.contigs… October 22, 2012
Octocat-spinner-32 formatmatrix.h added sets to amova and homova commands. added oligos to make.contigs… October 22, 2012
Octocat-spinner-32 formatphylip.cpp added sets to amova and homova commands. added oligos to make.contigs… October 22, 2012
Octocat-spinner-32 formatphylip.h added sets to amova and homova commands. added oligos to make.contigs… October 22, 2012
Octocat-spinner-32 fullmatrix.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 fullmatrix.h Revert to previous commit May 02, 2012
Octocat-spinner-32 geom.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 geom.h Revert to previous commit May 02, 2012
Octocat-spinner-32 getcommandinfocommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getcommandinfocommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getcoremicrobiomecommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 getcoremicrobiomecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getcurrentcommand.cpp added mergesfffiles command. added current directories to get.current… February 03, 2014
Octocat-spinner-32 getcurrentcommand.h added mergesfffiles command. added current directories to get.current… February 03, 2014
Octocat-spinner-32 getdistscommand.cpp added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 getdistscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 getgroupcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getgroupcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getgroupscommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 getgroupscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getlabelcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getlabelcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getlineagecommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 getlineagecommand.h added shared, constaxonomy and label parameter to get.lineage and rem… April 29, 2013
Octocat-spinner-32 getlistcountcommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 getlistcountcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getmetacommunitycommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 getmetacommunitycommand.h added rjsd calculator. improved work balance load between processors … January 21, 2014
Octocat-spinner-32 getmimarkspackagecommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 getmimarkspackagecommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 getopt_long.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 getopt_long.h Revert to previous commit May 02, 2012
Octocat-spinner-32 getotulabelscommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 getotulabelscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 getoturepcommand.cpp added Jensen-Shannon calc. working on get.communitytype command. fixe… January 09, 2014
Octocat-spinner-32 getoturepcommand.h added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 getotuscommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 getotuscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getrabundcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 getrabundcommand.h added count file to get.sabund and get.rabund commands. fixed bug in … April 03, 2013
Octocat-spinner-32 getrelabundcommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 getrelabundcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 getsabundcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 getsabundcommand.h added count file to get.sabund and get.rabund commands. fixed bug in … April 03, 2013
Octocat-spinner-32 getseqscommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 getseqscommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v… October 17, 2013
Octocat-spinner-32 getsharedotucommand.cpp fixes while testing 1.33.0 February 10, 2014
Octocat-spinner-32 getsharedotucommand.h working on chimera.uchime change for dereplicate=t bug. added shared … March 05, 2013
Octocat-spinner-32 goodscoverage.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 goodscoverage.h Revert to previous commit May 02, 2012
Octocat-spinner-32 gotohoverlap.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 gotohoverlap.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 gower.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 gower.h Revert to previous commit May 02, 2012
Octocat-spinner-32 groupmap.cpp added rename.seqs command. May 29, 2013
Octocat-spinner-32 groupmap.h added rename.seqs command. May 29, 2013
Octocat-spinner-32 hamming.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 hamming.h Revert to previous commit May 02, 2012
Octocat-spinner-32 hcluster.cpp changes while testing 1.27 August 06, 2012
Octocat-spinner-32 hcluster.h Revert to previous commit May 02, 2012
Octocat-spinner-32 hclustercommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 hclustercommand.h random stuff September 04, 2013
Octocat-spinner-32 heatmap.cpp pcr.seqs bug fix. working on shannon range calc February 28, 2014
Octocat-spinner-32 heatmap.h added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 heatmapcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 heatmapcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 heatmapsim.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 heatmapsim.h Revert to previous commit May 02, 2012
Octocat-spinner-32 heatmapsimcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 heatmapsimcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 heip.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 heip.h Revert to previous commit May 02, 2012
Octocat-spinner-32 hellinger.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 hellinger.h Revert to previous commit May 02, 2012
Octocat-spinner-32 helpcommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 helpcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 homovacommand.cpp <= change for anova and homova. finished chimera.uchime dereplicate=t… March 06, 2013
Octocat-spinner-32 homovacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 ignoregaps.h Revert to previous commit May 02, 2012
Octocat-spinner-32 indicatorcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 indicatorcommand.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato… May 06, 2013
Octocat-spinner-32 inputdata.cpp fixes while testing 1.33.0 February 10, 2014
Octocat-spinner-32 inputdata.h Revert to previous commit May 02, 2012
Octocat-spinner-32 interv.f Revert to previous commit May 02, 2012
Octocat-spinner-32 intrv.f Revert to previous commit May 02, 2012
Octocat-spinner-32 invsimpson.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 invsimpson.h Revert to previous commit May 02, 2012
Octocat-spinner-32 jackknife.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 jackknife.h Revert to previous commit May 02, 2012
Octocat-spinner-32 kmeans.cpp working on get.communitytype command January 29, 2014
Octocat-spinner-32 kmeans.h working on get.communitytype command January 29, 2014
Octocat-spinner-32 kmer.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 kmer.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 kmerdb.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 kmerdb.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 kmernode.cpp added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 kmernode.h added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 kmertree.cpp mods to resolve some misc warnings. added alignPrimer function to nee… February 27, 2013
Octocat-spinner-32 kmertree.h added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 knn.cpp added count file to get.groups and remove.groups. added shortcut para… September 11, 2012
Octocat-spinner-32 knn.h Revert to previous commit May 02, 2012
Octocat-spinner-32 kruskalwalliscommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 kruskalwalliscommand.h changes while testing October 02, 2013
Octocat-spinner-32 lefsecommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 lefsecommand.h changes while testing October 02, 2013
Octocat-spinner-32 libshuff.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 libshuff.h mods to resolve some misc warnings. added alignPrimer function to nee… February 27, 2013
Octocat-spinner-32 libshuffcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 libshuffcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 linearalgebra.cpp added Jensen-Shannon calc. working on get.communitytype command. fixe… January 09, 2014
Octocat-spinner-32 linearalgebra.h added Jensen-Shannon calc. working on get.communitytype command. fixe… January 09, 2014
Octocat-spinner-32 listotulabelscommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 listotulabelscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 listseqscommand.cpp added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v… October 17, 2013
Octocat-spinner-32 listseqscommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v… October 17, 2013
Octocat-spinner-32 listvector.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 listvector.hpp adding labels to list file. October 17, 2013
Octocat-spinner-32 loadlogfilecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 loadlogfilecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 logsd.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 logsd.h Revert to previous commit May 02, 2012
Octocat-spinner-32 macros.h a lot of new input parameters in rf module, implemented a pruning sys… May 02, 2013
Octocat-spinner-32 makebiomcommand.cpp fixed bug in make.biom with picrust that didn’t allow for unclassifie… February 25, 2014
Octocat-spinner-32 makebiomcommand.h added picrust and ref taxonomy parameters to make.biom October 22, 2013
Octocat-spinner-32 makecontigscommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 makecontigscommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 makefastqcommand.cpp added *.count.summary file to count.groups command. added deltaq and … February 06, 2013
Octocat-spinner-32 makefastqcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 makefile fixes while building February 12, 2014
Octocat-spinner-32 makegroupcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 makegroupcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 makelefsecommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 makelefsecommand.h added make.lefse command. fixed bug in make.contigs with trimming rev… June 13, 2013
Octocat-spinner-32 makelookupcommand.cpp changes while testing May 23, 2013
Octocat-spinner-32 makelookupcommand.h citation changes for 1.31.0 May 28, 2013
Octocat-spinner-32 maligner.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 maligner.h Revert to previous commit May 02, 2012
Octocat-spinner-32 manhattan.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 manhattan.h Revert to previous commit May 02, 2012
Octocat-spinner-32 mantelcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 mantelcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 matrixoutputcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 matrixoutputcommand.h added rjsd calculator. improved work balance load between processors … January 21, 2014
Octocat-spinner-32 memchi2.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 memchi2.h Revert to previous commit May 02, 2012
Octocat-spinner-32 memchord.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 memchord.h Revert to previous commit May 02, 2012
Octocat-spinner-32 memeuclidean.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 memeuclidean.h Revert to previous commit May 02, 2012
Octocat-spinner-32 mempearson.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 mempearson.h Revert to previous commit May 02, 2012
Octocat-spinner-32 mergefilecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 mergefilecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 mergegroupscommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 mergegroupscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 mergesfffilecommand.cpp added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 mergesfffilecommand.h added mergesfffiles command. added current directories to get.current… February 03, 2014
Octocat-spinner-32 mergetaxsummarycommand.cpp added merge.taxsummary command. added column format to dist.shared. February 13, 2013
Octocat-spinner-32 mergetaxsummarycommand.h added merge.taxsummary command. added column format to dist.shared. February 13, 2013
Octocat-spinner-32 metastatscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 metastatscommand.h changed name of get.metacommunity to get.communitytype. fixed bug in … August 14, 2013
Octocat-spinner-32 mgclustercommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 mgclustercommand.h Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 mothur.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 mothur.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 mothurfisher.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 mothurfisher.h Revert to previous commit May 02, 2012
Octocat-spinner-32 mothurmetastats.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 mothurmetastats.h changed name of get.metacommunity to get.communitytype. fixed bug in … August 14, 2013
Octocat-spinner-32 mothurout.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 mothurout.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 myPerseus.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 myPerseus.h Revert to previous commit May 02, 2012
Octocat-spinner-32 myseqdist.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 myseqdist.h Revert to previous commit May 02, 2012
Octocat-spinner-32 nameassignment.cpp fixed subsample name file name issue. added count parameter to cluste… July 30, 2012
Octocat-spinner-32 nameassignment.hpp fixed subsample name file name issue. added count parameter to cluste… July 30, 2012
Octocat-spinner-32 nast.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 nast.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 nastreport.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 nastreport.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 needlemanoverlap.cpp added adjustDots function to pcr.seqs, keeps sequences aligned in cas… April 26, 2013
Octocat-spinner-32 needlemanoverlap.hpp mods to resolve some misc warnings. added alignPrimer function to nee… February 27, 2013
Octocat-spinner-32 newcommandtemplate.cpp Test new machine. January 20, 2014
Octocat-spinner-32 newcommandtemplate.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 nmdscommand.cpp added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 nmdscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 noalign.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 noalign.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 nocommands.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 nocommands.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 normalizesharedcommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 normalizesharedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 npshannon.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 npshannon.h Revert to previous commit May 02, 2012
Octocat-spinner-32 nseqs.h Revert to previous commit May 02, 2012
Octocat-spinner-32 observable.h Revert to previous commit May 02, 2012
Octocat-spinner-32 odum.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 odum.h Revert to previous commit May 02, 2012
Octocat-spinner-32 oligos.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 oligos.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 onegapdist.h Revert to previous commit May 02, 2012
Octocat-spinner-32 onegapignore.h Revert to previous commit May 02, 2012
Octocat-spinner-32 optionparser.cpp added method parameter to get.oturep. options method=abundance or dis… April 05, 2013
Octocat-spinner-32 optionparser.h added load.logfile command. changed summary.single output for subsamp… June 19, 2012
Octocat-spinner-32 ordervector.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 ordervector.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 otuassociationcommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 otuassociationcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 otuhierarchycommand.cpp fixes while testing 1.33.0 February 10, 2014
Octocat-spinner-32 otuhierarchycommand.h fixes while testing 1.33.0 February 10, 2014
Octocat-spinner-32 overlap.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 overlap.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 pairwiseseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 pairwiseseqscommand.h added lefse command. added check for hard filter length. fixed bug in… September 18, 2013
Octocat-spinner-32 pam.cpp fixes while building February 12, 2014
Octocat-spinner-32 pam.h added mergesfffiles command. added current directories to get.current… February 03, 2014
Octocat-spinner-32 parsefastaqcommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 parsefastaqcommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 parselistscommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 parselistscommand.h modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 parsimony.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 parsimony.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato… May 06, 2013
Octocat-spinner-32 parsimonycommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 parsimonycommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 pcacommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 pcacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 pcoacommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 pcoacommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 pcrseqscommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 phylodiversitycommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 phylodiversitycommand.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato… May 06, 2013
Octocat-spinner-32 phylosummary.cpp added relabund parameter to classify.seqs and summary.tax commands February 04, 2014
Octocat-spinner-32 phylosummary.h added relabund parameter to classify.seqs and summary.tax commands February 04, 2014
Octocat-spinner-32 phylotree.cpp added picrust and ref taxonomy parameters to make.biom October 22, 2013
Octocat-spinner-32 phylotree.h added picrust and ref taxonomy parameters to make.biom October 22, 2013
Octocat-spinner-32 phylotypecommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 phylotypecommand.h added end of file character to some type type reads. fixes while test… April 01, 2013
Octocat-spinner-32 pintail.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 pintail.h random stuff September 04, 2013
Octocat-spinner-32 pipelinepdscommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 pipelinepdscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 prcseqscommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 preclustercommand.cpp pre.cluster unable to spawn necessary processes adjustment. April 09, 2014
Octocat-spinner-32 preclustercommand.h added mothurOutJustToScreen function and changed all counter outputs … April 19, 2013
Octocat-spinner-32 primerdesigncommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 primerdesigncommand.h modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 prng.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 prng.h Revert to previous commit May 02, 2012
Octocat-spinner-32 progress.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 progress.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 qFinderDMM.cpp Merge remote-tracking branch 'mothur/master' January 09, 2014
Octocat-spinner-32 qFinderDMM.h added Jensen-Shannon calc. working on get.communitytype command. fixe… January 09, 2014
Octocat-spinner-32 qstat.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 qstat.h Revert to previous commit May 02, 2012
Octocat-spinner-32 qualityscores.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 qualityscores.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 quitcommand.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 quitcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 rabundvector.cpp added shannonrange calc. March 05, 2014
Octocat-spinner-32 rabundvector.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 randomforest.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 randomforest.hpp adding misclassification output file September 11, 2013
Octocat-spinner-32 randomnumber.cpp added sparcc command. fixed bug in remove.groups that removed all gro… May 13, 2013
Octocat-spinner-32 randomnumber.h added sparcc command. fixed bug in remove.groups that removed all gro… May 13, 2013
Octocat-spinner-32 rarecalc.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 rarecalc.h Revert to previous commit May 02, 2012
Octocat-spinner-32 raredisplay.cpp changed how rarefaction commands find the lci and hci. they now save … May 17, 2013
Octocat-spinner-32 raredisplay.h changed how rarefaction commands find the lci and hci. they now save … May 17, 2013
Octocat-spinner-32 rarefact.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 rarefact.h forced rarefaction.single to output ending line for all groups. added… May 24, 2012
Octocat-spinner-32 rarefactcommand.cpp added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 rarefactcommand.h added shannonrange calc. March 05, 2014
Octocat-spinner-32 rarefactioncurvedata.h Revert to previous commit May 02, 2012
Octocat-spinner-32 rarefactsharedcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 rarefactsharedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 readblast.cpp added warning to readBlast to warn about duplicate names in the blast… December 14, 2012
Octocat-spinner-32 readblast.h fixed outputName creator, added debugging to readblast December 14, 2012
Octocat-spinner-32 readcluster.cpp added SequenceCountParser class to parse the count table by group. ad… August 08, 2012
Octocat-spinner-32 readcluster.h added SequenceCountParser class to parse the count table by group. ad… August 08, 2012
Octocat-spinner-32 readcolumn.cpp paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato… May 06, 2013
Octocat-spinner-32 readcolumn.h fixed subsample name file name issue. added count parameter to cluste… July 30, 2012
Octocat-spinner-32 readmatrix.hpp changes while testing 1.27 August 06, 2012
Octocat-spinner-32 readphylip.cpp fixed subsample name file name issue. added count parameter to cluste… July 30, 2012
Octocat-spinner-32 readphylip.h fixed subsample name file name issue. added count parameter to cluste… July 30, 2012
Octocat-spinner-32 readphylipvector.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 readphylipvector.h Revert to previous commit May 02, 2012
Octocat-spinner-32 readtree.cpp added name, group and count files to chop.seqs. added intelligent war… April 03, 2013
Octocat-spinner-32 readtree.h major change to the tree class to use the count table class instead o… September 07, 2012
Octocat-spinner-32 refchimeratest.cpp fixed seq. error align=f issue. added std and ave calcs to mothurout.… January 18, 2013
Octocat-spinner-32 refchimeratest.h Changes to seq.error so that an alignment is not necessary January 03, 2013
Octocat-spinner-32 referencedb.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 referencedb.h Revert to previous commit May 02, 2012
Octocat-spinner-32 regularizeddecisiontree.cpp added files for regularized random forest November 16, 2012
Octocat-spinner-32 regularizeddecisiontree.h added files for regularized random forest November 16, 2012
Octocat-spinner-32 regularizedrandomforest.cpp a lot of new input parameters in rf module, implemented a pruning sys… May 02, 2013
Octocat-spinner-32 regularizedrandomforest.h added files for regularized random forest November 16, 2012
Octocat-spinner-32 removedistscommand.cpp added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 removedistscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 removegroupscommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 removegroupscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 removelineagecommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 removelineagecommand.h added shared, constaxonomy and label parameter to get.lineage and rem… April 29, 2013
Octocat-spinner-32 removeotulabelscommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 removeotulabelscommand.h added get.dists and remove.dists commands. fixed bug in trim.seqs win… January 29, 2013
Octocat-spinner-32 removeotuscommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 removeotuscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 removerarecommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 removerarecommand.h added count file to get.sabund and get.rabund commands. fixed bug in … April 03, 2013
Octocat-spinner-32 removeseqscommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 removeseqscommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v… October 17, 2013
Octocat-spinner-32 renameseqscommand.cpp changes while testing October 02, 2013
Octocat-spinner-32 renameseqscommand.h added rename.seqs command. May 29, 2013
Octocat-spinner-32 reportfile.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 reportfile.h Revert to previous commit May 02, 2012
Octocat-spinner-32 reversecommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 reversecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 rftreenode.cpp a lot of new input parameters in rf module, implemented a pruning sys… May 02, 2013
Octocat-spinner-32 rftreenode.hpp a lot of new input parameters in rf module, implemented a pruning sys… May 02, 2013
Octocat-spinner-32 sabundvector.cpp added shannonrange calc. March 05, 2014
Octocat-spinner-32 sabundvector.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 screenseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 screenseqscommand.h added adjust parameter to mgcluster. fixed bug in classify.otu with c… July 18, 2013
Octocat-spinner-32 secondarystructurecommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 secondarystructurecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 sensspeccommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 sensspeccommand.h added square format for phylipfile. made command work with list files… April 29, 2013
Octocat-spinner-32 seqerrorcommand.cpp working on sra and get.mimarkspackage commands. added file parameter … April 02, 2014
Octocat-spinner-32 seqerrorcommand.h working on dereplicate=t issue in chimera.slayer and chimera.perseus,… March 18, 2013
Octocat-spinner-32 seqnoise.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 seqnoise.h Revert to previous commit May 02, 2012
Octocat-spinner-32 seqsummarycommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 seqsummarycommand.h added checks to make sure windows processes completed their tasks. January 28, 2013
Octocat-spinner-32 sequence.cpp added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 sequence.hpp added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 sequencecountparser.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 sequencecountparser.h added SequenceCountParser class to parse the count table by group. ad… August 08, 2012
Octocat-spinner-32 sequencedb.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sequencedb.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sequenceparser.cpp added count file to chimera.uchime. found issue with uchime program t… August 13, 2012
Octocat-spinner-32 sequenceparser.h added SequenceCountParser class to parse the count table by group. ad… August 08, 2012
Octocat-spinner-32 setcurrentcommand.cpp added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 setcurrentcommand.h added method parameter to get.oturep. options method=abundance or dis… April 05, 2013
Octocat-spinner-32 setdircommand.cpp added make.lefse command. fixed bug in make.contigs with trimming rev… June 13, 2013
Octocat-spinner-32 setdircommand.h added modify names parameter to set.dir May 17, 2013
Octocat-spinner-32 setlogfilecommand.cpp changes while testing October 02, 2013
Octocat-spinner-32 setlogfilecommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 sffinfocommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 sffinfocommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 sffmultiplecommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 sffmultiplecommand.h added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v… October 17, 2013
Octocat-spinner-32 sgram.f Revert to previous commit May 02, 2012
Octocat-spinner-32 shannon.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 shannon.h Revert to previous commit May 02, 2012
Octocat-spinner-32 shannoneven.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 shannoneven.h Revert to previous commit May 02, 2012
Octocat-spinner-32 shannonrange.cpp added shared file to make.table March 06, 2014
Octocat-spinner-32 shannonrange.h added shannonrange calc. March 05, 2014
Octocat-spinner-32 sharedace.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedace.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedanderbergs.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedanderbergs.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedbraycurtis.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedbraycurtis.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedchao1.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedchao1.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedcommand.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedcommand.h adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedjabund.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedjabund.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedjackknife.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedjackknife.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedjclass.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedjclass.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedjest.cpp changes while testing October 02, 2013
Octocat-spinner-32 sharedjest.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedjsd.cpp converted jsd calculation to be based on relative abundance January 09, 2014
Octocat-spinner-32 sharedjsd.h added Jensen-Shannon calc. working on get.communitytype command. fixe… January 09, 2014
Octocat-spinner-32 sharedkstest.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedkstest.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedkulczynski.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedkulczynski.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedkulczynskicody.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedkulczynskicody.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedlennon.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedlennon.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedlistvector.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedlistvector.h adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedmarczewski.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedmarczewski.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedmorisitahorn.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedmorisitahorn.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharednseqs.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedochiai.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedochiai.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedordervector.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedordervector.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedrabundfloatvector.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedrabundfloatvector.h added sparcc command. fixed bug in remove.groups that removed all gro… May 13, 2013
Octocat-spinner-32 sharedrabundvector.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedrabundvector.h added get.metacommunity command. April 12, 2013
Octocat-spinner-32 sharedrjsd.cpp added rjsd calculator. improved work balance load between processors … January 21, 2014
Octocat-spinner-32 sharedrjsd.h added rjsd calculator. improved work balance load between processors … January 21, 2014
Octocat-spinner-32 sharedsabundvector.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsabundvector.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsobs.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsobs.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsobscollectsummary.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 sharedsobscollectsummary.h added sharedotu parameter to venn command. working of make.contigs. December 18, 2012
Octocat-spinner-32 sharedsorabund.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsorabund.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsorclass.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsorclass.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsorest.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedsorest.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedthetan.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedthetan.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedthetayc.cpp added filter.shared command. fixed lci and uci for thetayc calc January 04, 2013
Octocat-spinner-32 sharedthetayc.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sharedutilities.cpp fixed issue in tree.shared when shared file was not sorted December 17, 2012
Octocat-spinner-32 sharedutilities.h Revert to previous commit May 02, 2012
Octocat-spinner-32 shen.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 shen.h Revert to previous commit May 02, 2012
Octocat-spinner-32 shhhercommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 shhhercommand.h added order=A or order=B to trim.flows and shhh.flows commands. added… February 12, 2013
Octocat-spinner-32 shhhseqscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 shhhseqscommand.h added checks to make sure windows processes completed their tasks. January 28, 2013
Octocat-spinner-32 simpson.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 simpson.h Revert to previous commit May 02, 2012
Octocat-spinner-32 simpsoneven.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 simpsoneven.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sinerp.f Revert to previous commit May 02, 2012
Octocat-spinner-32 singlelinkage.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 slayer.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 slayer.h Revert to previous commit May 02, 2012
Octocat-spinner-32 slibshuff.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 slibshuff.h Revert to previous commit May 02, 2012
Octocat-spinner-32 smithwilson.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 smithwilson.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sobs.h Revert to previous commit May 02, 2012
Octocat-spinner-32 soergel.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 soergel.h Revert to previous commit May 02, 2012
Octocat-spinner-32 solow.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 solow.h Revert to previous commit May 02, 2012
Octocat-spinner-32 sortseqscommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 sortseqscommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 sparcccommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 sparcccommand.h citation changes for 1.31.0 May 28, 2013
Octocat-spinner-32 sparsedistancematrix.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 sparsedistancematrix.h Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 sparsematrix.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 sparsematrix.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 spearman.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 spearman.h Revert to previous commit May 02, 2012
Octocat-spinner-32 speciesprofile.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 speciesprofile.h Revert to previous commit May 02, 2012
Octocat-spinner-32 spline.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 spline.h Revert to previous commit May 02, 2012
Octocat-spinner-32 splitabundcommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 splitabundcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 splitgroupscommand.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 splitgroupscommand.h added topdown parameter to pre.cluster. added more debugging output t… January 16, 2013
Octocat-spinner-32 splitmatrix.cpp added sparcc command. fixed bug in remove.groups that removed all gro… May 13, 2013
Octocat-spinner-32 splitmatrix.h added count file to cluster.classic and cluster.split. modified split… July 31, 2012
Octocat-spinner-32 sracommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 sracommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 sslvrg.f Revert to previous commit May 02, 2012
Octocat-spinner-32 structchi2.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 structchi2.h Revert to previous commit May 02, 2012
Octocat-spinner-32 structchord.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 structchord.h Revert to previous commit May 02, 2012
Octocat-spinner-32 structeuclidean.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 structeuclidean.h Revert to previous commit May 02, 2012
Octocat-spinner-32 structkulczynski.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 structkulczynski.h Revert to previous commit May 02, 2012
Octocat-spinner-32 structpearson.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 structpearson.h Revert to previous commit May 02, 2012
Octocat-spinner-32 stxwx.f Revert to previous commit May 02, 2012
Octocat-spinner-32 subsample.cpp adding labels to list file. October 17, 2013
Octocat-spinner-32 subsample.h added classify.shared command and random forest files. added count fi… October 02, 2012
Octocat-spinner-32 subsamplecommand.cpp modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 subsamplecommand.h modifications to commands to add headers to list file. October 18, 2013
Octocat-spinner-32 suffixdb.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 suffixdb.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 suffixnodes.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 suffixnodes.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 suffixtree.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 suffixtree.hpp Revert to previous commit May 02, 2012
Octocat-spinner-32 summarycommand.cpp added shannonrange calc. March 05, 2014
Octocat-spinner-32 summarycommand.h added shannonrange calc. March 05, 2014
Octocat-spinner-32 summaryqualcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 summaryqualcommand.h added checks to make sure windows processes completed their tasks. January 28, 2013
Octocat-spinner-32 summarysharedcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 summarysharedcommand.h added rjsd calculator. improved work balance load between processors … January 21, 2014
Octocat-spinner-32 summarytaxcommand.cpp added relabund parameter to classify.seqs and summary.tax commands February 04, 2014
Octocat-spinner-32 summarytaxcommand.h added relabund parameter to classify.seqs and summary.tax commands February 04, 2014
Octocat-spinner-32 systemcommand.cpp fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 systemcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 taxonomyequalizer.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 taxonomyequalizer.h Revert to previous commit May 02, 2012
Octocat-spinner-32 taxonomynode.cpp added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 taxonomynode.h added zap method to classify.seqs and changed bayesian method name to… October 03, 2012
Octocat-spinner-32 tree.cpp added name, group and count files to chop.seqs. added intelligent war… April 03, 2013
Octocat-spinner-32 tree.h added name, group and count files to chop.seqs. added intelligent war… April 03, 2013
Octocat-spinner-32 treecalculator.h Revert to previous commit May 02, 2012
Octocat-spinner-32 treegroupscommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 treegroupscommand.h added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 treemap.cpp added count file to get.oturep, pre.cluster, screen.seqs, tree.shared… September 25, 2012
Octocat-spinner-32 treemap.h major change to the tree class to use the count table class instead o… September 07, 2012
Octocat-spinner-32 treenode.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 treenode.h Revert to previous commit May 02, 2012
Octocat-spinner-32 treereader.cpp added otulabels to heatmap.bin. made OTUlabels “smarter” so OTU01 and… October 08, 2013
Octocat-spinner-32 treereader.h major change to the tree class to use the count table class instead o… September 07, 2012
Octocat-spinner-32 trialSwap2.cpp mods to resolve some misc warnings. added alignPrimer function to nee… February 27, 2013
Octocat-spinner-32 trialswap2.h added functions to calculate standard deviation and zscore May 15, 2012
Octocat-spinner-32 trimflowscommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 trimflowscommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 trimoligos.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 trimoligos.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 trimseqscommand.cpp added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 trimseqscommand.h added oligos class. added check orient parameter to trim.flows, sffin… April 09, 2014
Octocat-spinner-32 unifracunweightedcommand.cpp added lefse command. added check for hard filter length. fixed bug in… September 18, 2013
Octocat-spinner-32 unifracunweightedcommand.h fixed bug in phylo.diversity rooting. added filename patterns and cre… December 13, 2012
Octocat-spinner-32 unifracweightedcommand.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 unifracweightedcommand.h added lefse command. added check for hard filter length. fixed bug in… September 18, 2013
Octocat-spinner-32 unweighted.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 unweighted.h paralellized parsimony, unifrac.unweighted, phylo.diversity, indicato… May 06, 2013
Octocat-spinner-32 uvest.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 uvest.h Revert to previous commit May 02, 2012
Octocat-spinner-32 validcalculator.cpp added mothurgetpid function. fixed bug with align.seqs related to g++… March 25, 2014
Octocat-spinner-32 validcalculator.h Revert to previous commit May 02, 2012
Octocat-spinner-32 validparameter.cpp major change to the tree class to use the count table class instead o… September 07, 2012
Octocat-spinner-32 validparameter.h Revert to previous commit May 02, 2012
Octocat-spinner-32 venn.cpp added fastq to list.seqs, get.seqs and remove.seqs. fixed bug where v… October 17, 2013
Octocat-spinner-32 venn.h added sharedotu parameter to venn command. working of make.contigs. December 18, 2012
Octocat-spinner-32 venncommand.cpp fixes while testing 1.33.0 February 10, 2014
Octocat-spinner-32 venncommand.h added binary file operations to mothurout class. added comment to seq… November 19, 2013
Octocat-spinner-32 weighted.cpp changed int to pid_t type in fork(). roughed in get.mimarkscommand. March 25, 2014
Octocat-spinner-32 weighted.h paralellized unifrac.weighted for windows. added get.metacommunity co… April 19, 2013
Octocat-spinner-32 weightedlinkage.cpp Update mgcluster to use dist=1 for missing distances when no cutoff i… July 19, 2013
Octocat-spinner-32 whittaker.cpp Revert to previous commit May 02, 2012
Octocat-spinner-32 whittaker.h Revert to previous commit May 02, 2012
Octocat-spinner-32 wilcox.cpp changed name of get.metacommunity to get.communitytype. fixed bug in … August 14, 2013
Octocat-spinner-32 wilcox.h changed name of get.metacommunity to get.communitytype. fixed bug in … August 14, 2013
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