Version 1.36.0

New commands

• set.seed - allows you to seed random.
• make.file- creates a file containing list of fastq or gz files for input to make.contigs.

Feature updates

• pre.cluster - added cluster method for unaligned sequences. Added align, mismatch, match, gapopen, gapextend parameters.
• set.dir - if output directory does not exist mothur will create it for you.
• chimera.uchime - adds method tag to output files. - http://www.mothur.org/forum/viewtopic.php?f=5&t=3636&p=10748#p10748
• chop.seqs - adds qfile option to allows for chopping quality files.
• classify.otu - adds threshold parameter. The threshold parameter allows you to specify a cutoff for the taxonomy file that is being inputted.
• rename.seqs - adds count, delim, and placement parameters.
• seed parameter added to all commands to allow you to easily seed random while running commands.
• make.shared - mothur no longer checks for biom matrix type to allow for more flexibility.
• make.shared - rabund files are no longer outputted. Mothur will create a rabund file with the [[get.rabund]] command.
• set.dir - if output directory does not exist it will be created.
• no longer create a log file simple command line option runs of mothur
• make.sra - allow for assigning multiple sets of files to the same group in 3 column format.
• make.contigs - allow for missing reads in files.
• metastats - remove qvalues. Also removes fortran source from mothur.
• automatically adjust number of processors when fork() fails
• Removes extra white spaces from mothur's print to make output files more compatible with other software packages. - http://www.mothur.org/forum/viewtopic.php?f=4&t=3703
• degap.seqs - adds the processors option.
• Adds column headers to Design File
• phylo.diversity - adds sampledepth parameter. - http://www.mothur.org/forum/viewtopic.php?f=3&t=3320
• set.dir - Sets tempdefault location to mothur's executable location to help reduce "unable to find file" errors.
• make.contigs - allow for gzipped version for fastq files as inputs.
• Added file parameter to saved files by mothur. file=current can now be used.

Bug fixes

• metastats - infinite loop with certain datasets - http://www.mothur.org/forum/viewtopic.php?f=3&t=3701
• cluster.split - did not allow you to use the classic option with the file option.
• make.biom - repeat labels when combining mothur OTU labels with non mothur OTU labels, this can results in a duplicate "simple" label. This causes an incorrect taxonomy to be assigned to the OTU.
• remove.groups - not creating a list file for each label.
• make.biom - remove paths from filenames to make compliant with qiime parser. - http://www.mothur.org/forum/viewtopic.php?f=3&t=3781&p=11241#p11241
• sffinfo - off by one in right side trimming. http://www.mothur.org/forum/viewtopic.php?f=4&t=3764
• make.contigs - Bug Fix - when using index files in version 1.35 quality data was over trimmed by the length of the barcode.