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2010-05-12	westcott	modified freq parameter be a percentage of numSeqs...	commit \| commitdiff \| tree
2010-05-11	westcott	added clearcut command	commit \| commitdiff \| tree
2010-05-10	westcott	added chop.seqs command	commit \| commitdiff \| tree
2010-05-10	westcott	fixed problem with class.fy.seqs where group totals...	commit \| commitdiff \| tree
2010-05-10	westcott	added make.group command	commit \| commitdiff \| tree
2010-05-10	westcott	worked on trim.seqs	commit \| commitdiff \| tree
2010-05-10	westcott	worked on trim.seqs	commit \| commitdiff \| tree
2010-05-07	westcott	changed confidence scores calculation in bayesian	commit \| commitdiff \| tree
2010-05-07	westcott	modified trim.seqs to account for primers of different...	commit \| commitdiff \| tree
2010-05-07	westcott	added diffs to trim.seqs	commit \| commitdiff \| tree
2010-05-07	westcott	working on trim.seqs	commit \| commitdiff \| tree
2010-05-07	westcott	changed groupfile in classify.seqs to reflect multiple...	commit \| commitdiff \| tree
2010-05-05	westcott	filled out reference taxonomy with "unclassified" so...	commit \| commitdiff \| tree
2010-05-04	westcott	enabled ~	commit \| commitdiff \| tree
2010-05-04	westcott	fixed bug that caused bayesian cutoff not to work if...	commit \| commitdiff \| tree
2010-05-04	westcott	added phylo.diversity command. added hard parameter...	commit \| commitdiff \| tree
2010-04-30	westcott	made get.oturep more memory efficient by breaking the...	commit \| commitdiff \| tree
2010-04-30	westcott	paralellized trim.seqs	commit \| commitdiff \| tree
2010-04-29	westcott	paralellized summary.seqs and added mpi code to it.	commit \| commitdiff \| tree
2010-04-29	westcott	paralellized screen.seqs and added mpi code to it....	commit \| commitdiff \| tree
2010-04-28	westcott	added set.logfile command	commit \| commitdiff \| tree
2010-04-27	westcott	added name parameter to phylotype command	commit \| commitdiff \| tree
2010-04-27	westcott	reworked the classifiers summary file added groupfile...	commit \| commitdiff \| tree
2010-04-26	westcott	made classifier faster	commit \| commitdiff \| tree
2010-04-20	westcott	a few modifications for 1.9	commit \| commitdiff \| tree
2010-04-20	westcott	a few modifications for 1.9	commit \| commitdiff \| tree
2010-04-17	westcott	1.9	commit \| commitdiff \| tree
2010-04-16	westcott	1.9	commit \| commitdiff \| tree
2010-04-14	westcott	some changes while testing 1.9	commit \| commitdiff \| tree
2010-04-07	westcott	added MPI code, broke up chimera.seqs into 5 separated...	commit \| commitdiff \| tree
2010-03-17	westcott	finished mpi for filter.seqs	commit \| commitdiff \| tree
2010-03-17	westcott	testing	commit \| commitdiff \| tree
2010-03-16	westcott	modified mpi code to save ram by writing out every...	commit \| commitdiff \| tree
2010-03-12	westcott	added MPI to dist.seqs command	commit \| commitdiff \| tree
2010-03-11	westcott	testing mpi	commit \| commitdiff \| tree
2010-03-04	westcott	mothur with external build	commit \| commitdiff \| tree
2010-03-04	westcott	changes to filter.seqs	commit \| commitdiff \| tree
2010-03-03	westcott	added checks for ^C to quit command instead of program	commit \| commitdiff \| tree
2010-03-01	westcott	adding mothurout.h and .cpp to repo	commit \| commitdiff \| tree
2010-02-26	westcott	filter.seqs can now accept multiple fasta files	commit \| commitdiff \| tree
2010-02-26	westcott	created mothurOut class to handle logfiles	commit \| commitdiff \| tree
2010-02-25	westcott	added parse.list command	commit \| commitdiff \| tree
2010-02-24	westcott	finished chimera changes	commit \| commitdiff \| tree
2010-02-23	westcott	added warning about merging with something above cutoff...	commit \| commitdiff \| tree
2010-02-23	westcott	added warning about merging with something above cutoff...	commit \| commitdiff \| tree
2010-02-22	westcott	chimeras, fix to sabundvector and sharedsabundvector...	commit \| commitdiff \| tree
2010-02-17	westcott	chimeras	commit \| commitdiff \| tree
2010-02-16	westcott	chimeracode	commit \| commitdiff \| tree
2010-02-12	westcott	working on chimeras	commit \| commitdiff \| tree
2010-02-03	westcott	added name option to read.tree for use in unifrac and...	commit \| commitdiff \| tree
2010-02-02	westcott	fixed bugs for 1.8	commit \| commitdiff \| tree
2010-01-28	westcott	fixed some bugs found while testing 1.8	commit \| commitdiff \| tree
2010-01-27	westcott	fixed some bugs found while testing 1.8	commit \| commitdiff \| tree
2010-01-27	westcott	added distance search method to classify.seqs	commit \| commitdiff \| tree
2010-01-26	westcott	added set.dir command and modified commands to redirect...	commit \| commitdiff \| tree
2010-01-19	westcott	added out.hierarchy command	commit \| commitdiff \| tree
2010-01-19	westcott	added warning about average neighbor merges around...	commit \| commitdiff \| tree
2010-01-14	westcott	added formatmatrix, formatcolumn, and formatphylip...	commit \| commitdiff \| tree
2010-01-12	westcott	worked on hcluster. made .single command run using...	commit \| commitdiff \| tree
2010-01-05	westcott	you can now use a distance matrix as input for the...	commit \| commitdiff \| tree
2010-01-04	westcott	added pca command	commit \| commitdiff \| tree
2009-12-23	westcott	added average and nearest neighbor methods to hcluster	commit \| commitdiff \| tree
2009-12-23	westcott	precluster command finished	commit \| commitdiff \| tree
2009-12-21	westcott	fixed some bugs and added mgcluster command	commit \| commitdiff \| tree
2009-12-09	westcott	added sorted parameter to get.oturep, added error checking...	commit \| commitdiff \| tree
2009-12-08	westcott	added list parameter to get.seqs and remove.seqs and...	commit \| commitdiff \| tree
2009-12-02	westcott	modified sequence class to read fasta files with comments...	commit \| commitdiff \| tree
2009-11-25	westcott	a few changes to chimera classes	commit \| commitdiff \| tree
2009-11-24	westcott	changed get.sharedotu to get.sharedseqs	commit \| commitdiff \| tree
2009-11-24	westcott	changed get.sharedotu to get.sharedseqs	commit \| commitdiff \| tree
2009-11-24	westcott	fixed bug in hcluster command	commit \| commitdiff \| tree
2009-11-23	westcott	edited taxonomy equalizer to fix bug with windows	commit \| commitdiff \| tree
2009-11-23	westcott	updated phylotype command	commit \| commitdiff \| tree
2009-11-23	westcott	changed label outputs for phylotype command	commit \| commitdiff \| tree
2009-11-23	westcott	added phylotype command which reads a taxonomy file...	commit \| commitdiff \| tree
2009-11-19	westcott	fixed bug in libshuff	commit \| commitdiff \| tree
2009-11-17	westcott	final fixes for 1.7	commit \| commitdiff \| tree
2009-11-13	westcott	finished work on classify.seqs bayesian method and...	commit \| commitdiff \| tree
2009-11-05	westcott	started work on classify.seqs command. changed the...	commit \| commitdiff \| tree
2009-11-02	westcott	added groups option to read.otu, added qtrim option...	commit \| commitdiff \| tree
2009-10-29	westcott	fixed bug with hcluster	commit \| commitdiff \| tree
2009-10-29	westcott	added hcluster command and fixed some bugs, namely...	commit \| commitdiff \| tree
2009-10-12	westcott	finished chimeraslayer method and added get.listcount...	commit \| commitdiff \| tree
2009-09-29	westcott	working on chimeraslayer and found bug in shared command.	commit \| commitdiff \| tree
2009-09-28	westcott	started adding chimeraslayer method and fixed minor...	commit \| commitdiff \| tree
2009-09-23	westcott	added get.sharedotu command	commit \| commitdiff \| tree
2009-09-22	westcott	removed line option	commit \| commitdiff \| tree
2009-09-21	westcott	align.check command added	commit \| commitdiff \| tree
2009-09-18	westcott	adding more error checking for list and group files...	commit \| commitdiff \| tree
2009-09-18	westcott	removing extra file output from pintail	commit \| commitdiff \| tree
2009-09-17	westcott	added check for blank files in openInputFile, add check...	commit \| commitdiff \| tree
2009-09-15	westcott	fixed some issues while testing 1.6	commit \| commitdiff \| tree
2009-09-14	westcott	added help to chimera.seqs	commit \| commitdiff \| tree
2009-09-11	westcott	chimeracheck method added	commit \| commitdiff \| tree
2009-09-09	westcott	continued work on chimeras and fixed bug in trim.seqs...	commit \| commitdiff \| tree
2009-09-08	westcott	finished with ccode, returned bellerophon to last save...	commit \| commitdiff \| tree
2009-09-04	westcott	changed reporting in ccode to only report those who...	commit \| commitdiff \| tree
2009-09-04	westcott	ccode working - still need to paralellize	commit \| commitdiff \| tree
2009-09-02	westcott	updated pats contact and mothur header info	commit \| commitdiff \| tree
2009-09-01	westcott	changed raredisplay to use vectors instead of files	commit \| commitdiff \| tree
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Mothur--16S microbiota sequencing software; mirror of main repository with my branches

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