git.donarmstrong.com Git - mothur.git/search

]> git.donarmstrong.com Git - mothur.git/search

2012-09-12	Sarah Westcott	optimizing classify.seqs calculating of template probabilities.	commit \| commitdiff \| tree
2012-09-11	Sarah Westcott	added count file to get.groups and remove.groups. added...	commit \| commitdiff \| tree
2012-09-07	Sarah Westcott	major change to the tree class to use the count table...	commit \| commitdiff \| tree
2012-08-24	Sarah Westcott	added sff.multiple command. fixed issue with windows...	commit \| commitdiff \| tree
2012-08-21	Sarah Westcott	added oligos, pdiffs, bdiffs, ldiffs, sdiffs, tiffs...	commit \| commitdiff \| tree
2012-08-14	Sarah Westcott	added code to format fast files for uchime. started...	commit \| commitdiff \| tree
2012-08-13	Sarah Westcott	added count file to chimera.uchime. found issue with...	commit \| commitdiff \| tree
2012-08-08	Sarah Westcott	added count parameter to chimera.slayer command	commit \| commitdiff \| tree
2012-08-08	Sarah Westcott	added SequenceCountParser class to parse the count...	commit \| commitdiff \| tree
2012-08-06	Sarah Westcott	changes while testing 1.27	commit \| commitdiff \| tree
2012-08-01	Sarah Westcott	paralellized chop.seqs	commit \| commitdiff \| tree
2012-07-31	Sarah Westcott	added count file to cluster.classic and cluster.split...	commit \| commitdiff \| tree
2012-07-30	Sarah Westcott	fixed subsample name file name issue. added count...	commit \| commitdiff \| tree
2012-07-27	Sarah Westcott	added sparseDistanceMatrix class. Modified cluster...	commit \| commitdiff \| tree
2012-07-11	Sarah Westcott	working on adding count file to mgcluster	commit \| commitdiff \| tree
2012-07-11	Sarah Westcott	working on mgcluster count file change	commit \| commitdiff \| tree
2012-07-11	Sarah Westcott	Merge remote-tracking branch 'origin/master'	commit \| commitdiff \| tree
2012-07-11	Sarah Westcott	added debug statements to trim.seqs	commit \| commitdiff \| tree
2012-07-10	Sarah Westcott	changes while testing 1.26	commit \| commitdiff \| tree
2012-07-03	Sarah Westcott	changes while testing 1.26	commit \| commitdiff \| tree
2012-06-28	Sarah Westcott	added countable class to read and store count file...	commit \| commitdiff \| tree
2012-06-26	Sarah Westcott	Merge remote-tracking branch 'origin/master'	commit \| commitdiff \| tree
2012-06-26	Sarah Westcott	made make.table alias to count.seqs command. added...	commit \| commitdiff \| tree
2012-06-19	Sarah Westcott	added phylip as output file type for commands that...	commit \| commitdiff \| tree
2012-06-19	Sarah Westcott	added load.logfile command. changed summary.single...	commit \| commitdiff \| tree
2012-06-12	Sarah Westcott	changed reading of name file to use buffered reads...	commit \| commitdiff \| tree
2012-06-11	Sarah Westcott	fixed bug with dist.shared subsampling. added mode...	commit \| commitdiff \| tree
2012-06-05	Sarah Westcott	added forward and reverse barcodes to trim.seqs to...	commit \| commitdiff \| tree
2012-06-04	Sarah Westcott	fixed classify.seqs output file name - had issue if...	commit \| commitdiff \| tree
2012-06-04	Sarah Westcott	added check to make sure shhh.flows child processes...	commit \| commitdiff \| tree
2012-05-29	Sarah Westcott	added code to check path for uchime and catchall executables	commit \| commitdiff \| tree
2012-05-24	Sarah Westcott	forced rarefaction.single to output ending line for...	commit \| commitdiff \| tree
2012-05-24	Sarah Westcott	fixed bug in sffinfo when ~ was used in the sff filename...	commit \| commitdiff \| tree
2012-05-23	Sarah Westcott	added metadata parameter to otu.association	commit \| commitdiff \| tree
2012-05-23	Sarah Westcott	added design and sets parameters to the rarefaction...	commit \| commitdiff \| tree
2012-05-22	Sarah Westcott	added debug output classify.seqs. worked on make.contigs...	commit \| commitdiff \| tree
2012-05-21	Sarah Westcott	added get.otulabels and remove.otulabels commands per...	commit \| commitdiff \| tree
2012-05-18	Sarah Westcott	added threshold parameter to make.contigs command.	commit \| commitdiff \| tree
2012-05-18	Sarah Westcott	Merge remote-tracking branch 'origin/master'	commit \| commitdiff \| tree
2012-05-18	Sarah Westcott	added check to cluster.classic to make sure file type...	commit \| commitdiff \| tree
2012-05-16	Sarah Westcott	added classic parameter to cluster.split. working...	commit \| commitdiff \| tree
2012-05-15	Sarah Westcott	added list.labels command. started work on make.contigs...	commit \| commitdiff \| tree
2012-05-14	Sarah Westcott	last checkin for 1.25.1	commit \| commitdiff \| tree
2012-05-14	Sarah Westcott	fixed bug in make.biom that occurred if some taxonomies...	commit \| commitdiff \| tree
2012-05-14	Sarah Westcott	Merge remote-tracking branch 'origin/master'	commit \| commitdiff \| tree
2012-05-14	Sarah Westcott	added debug info to engines function to get mother...	commit \| commitdiff \| tree
2012-05-11	Sarah Westcott	added some debug stuff to chimera.uchime. optimized...	commit \| commitdiff \| tree
2012-05-11	Sarah Westcott	fixed path redirect issue in shhh.flows. optimized...	commit \| commitdiff \| tree
2012-05-10	Sarah Westcott	fixed typos	commit \| commitdiff \| tree
2012-05-10	Sarah Westcott	added abundance and sample parameters to get.coremicrobiome...	commit \| commitdiff \| tree
2012-05-09	Sarah Westcott	working on get.coremicrobiom	commit \| commitdiff \| tree
2012-05-09	Sarah Westcott	cluster.split split method defaults to classify if...	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	fixed segfault in unifrac with subsample. in progress...	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	Revert to previous commit	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	fixing	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	moving source to source folder	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	moved mothur's source into a folder to make grabbing...	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	removing chime source files from mother project.	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	another test	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	test2	commit \| commitdiff \| tree
2012-05-02	Sarah Westcott	test commit	commit \| commitdiff \| tree
2012-05-01	Sarah Westcott	Merge remote-tracking branch 'mothur/master'	commit \| commitdiff \| tree
2012-05-01	Sarah Westcott	bug in dist.shared and tree.shared with new subsampling...	commit \| commitdiff \| tree
2012-05-01	Sarah Westcott	changes while testing	commit \| commitdiff \| tree
2012-05-01	Sarah Westcott	Merge remote-tracking branch 'mothur/master'	commit \| commitdiff \| tree
2012-05-01	Sarah Westcott	fixed bug in rarefaction.single creating the groups...	commit \| commitdiff \| tree
2012-04-30	Sarah Westcott	changes while testing	commit \| commitdiff \| tree
2012-04-30	Sarah Westcott	Merge remote-tracking branch 'mothur/master'	commit \| commitdiff \| tree
2012-04-30	Sarah Westcott	changes while testing	commit \| commitdiff \| tree
2012-04-27	Sarah Westcott	Merge remote-tracking branch 'mothur/master'	commit \| commitdiff \| tree
2012-04-27	Sarah Westcott	changes while testing.	commit \| commitdiff \| tree
2012-04-23	Sarah Westcott	bugs found while testing	commit \| commitdiff \| tree
2012-04-23	Sarah Westcott	added check for positive values in pairwise.seqs gap...	commit \| commitdiff \| tree
2012-04-20	Sarah Westcott	added uchime_src folder. added biom parameter to make...	commit \| commitdiff \| tree
2012-04-17	Sarah Westcott	added make.biom command	commit \| commitdiff \| tree
2012-04-16	Sarah Westcott	added subsample and consensus parameters to unifrac...	commit \| commitdiff \| tree
2012-04-13	Sarah Westcott	fixing out labels to match those in shared file. If...	commit \| commitdiff \| tree
2012-04-13	Sarah Westcott	added tree reader class to handle reading trees. Reworked...	commit \| commitdiff \| tree
2012-04-11	Sarah Westcott	fixed bug with windows version of trim.seqs when run...	commit \| commitdiff \| tree
2012-04-11	Sarah Westcott	added subsample and consensus parameters to unifrac...	commit \| commitdiff \| tree
2012-04-05	Sarah Westcott	adding uchime source	commit \| commitdiff \| tree
2012-04-05	Sarah Westcott	deleted consensus command	commit \| commitdiff \| tree
2012-04-05	Sarah Westcott	added subsample, tiers and processors to tree.shared...	commit \| commitdiff \| tree
2012-04-03	Sarah Westcott	fixed bug in corr.axes so that it now uses the shared...	commit \| commitdiff \| tree
2012-04-03	Sarah Westcott	working on adding subsampling to dist.shared. fixed...	commit \| commitdiff \| tree
2012-04-02	Sarah Westcott	added create.database command. fixed help in get.sharedseqs...	commit \| commitdiff \| tree
2012-03-28	Sarah Westcott	mods to pcr.seqs	commit \| commitdiff \| tree
2012-03-28	Sarah Westcott	added keep dots to pcr.seqs. fixed pre.cluster name...	commit \| commitdiff \| tree
2012-03-28	Sarah Westcott	minor changes to pcr.seqs. Added filterToPos and filterFrom...	commit \| commitdiff \| tree
2012-03-27	Sarah Westcott	initialized numLinkers and numSpacers in trim.seqs...	commit \| commitdiff \| tree
2012-03-27	Sarah Westcott	added pcr.seqs command. fixed bug in rarefacftion.single...	commit \| commitdiff \| tree
2012-03-13	Sarah Westcott	fixed makefile	commit \| commitdiff \| tree
2012-03-13	Sarah Westcott	bug fix in linear algebra that caused an infinite loop	commit \| commitdiff \| tree
2012-03-13	Sarah Westcott	added unix to ifdefs. minor changes while testing 1...	commit \| commitdiff \| tree
2012-03-07	Sarah Westcott	fixed pvalues for otu.association and corr.axes, fixed...	commit \| commitdiff \| tree
2012-03-06	Sarah Westcott	changed sffinfo flow default to true. fixed bug in...	commit \| commitdiff \| tree
2012-03-05	Sarah Westcott	fixed classify.seq error message when flip accnos file...	commit \| commitdiff \| tree
2012-03-02	Sarah Westcott	added cooccurence command	commit \| commitdiff \| tree
2012-02-29	Sarah Westcott	paralellized metastats for windows	commit \| commitdiff \| tree
2012-02-28	Sarah Westcott	paralellized dist.shared for windows	commit \| commitdiff \| tree
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Mothur--16S microbiota sequencing software; mirror of main repository with my branches

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