New Commands

Feature Updates

• Changes default clustering method to opti.
• Adds agc and dgc vsearch clustering methods for Windows users. #215
• Adds chimera.vsearch command for Windows users. #215
• Major speed improvement for pre.cluster command with aligned files. #220
• Major memory requirement reduction for pre.cluster command with by group option. #220
• Adds constaxonomy file to current files saved by mothur.
• Control-C handling: In script or batch mode exit mothur. In interactive mode exit command. #212 http://www.mothur.org/forum/viewtopic.php?f=5&t=4102&p=12431#p12431
• Adds blastdir parameter to set.dir command. #223
• Taxonomy files can now contain spaces in the taxon names. #265
• Makes refasta and repnames parameters optional for create.database command. #32
• Removes cutoff adjust in dist.seqs command. #274
• Adds trim parameter to make.sra command for use with sff files.

Bug Fixes

• Fixes Windows multiple processors with groups crash - chimera.uchime command.
• Fixes Windows bug with make.file command. #255
• Creates unique group names for 3 column format make.file command. #270
• Fixes bug with number of "taxon"_unclassifeds appended to taxonomy in classify.seqs.
• Eliminates zero abundance OTUs created by some floating point biom files converted to shared files make.shared.
• Floating point exception in sparcc command.
• Fixes bug where mothur was not finding matches for sequence names "off by one character" in the name. make.contigs
• Fixes bug with "find" command for Linux user in make.file
• Fixes bug with optimize parameter using alignreport file in screen.seqs command. #288

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Binaries

• Mac Version requires OSX 10.12 or higher