Mothur seeks to develop a single piece of open-source, expandable software to fill the bioinformatics needs of the microbial ecology community. It currently incorporates the functionality of dotur, sons, treeclimber, s-libshuff, unifrac, and more. In addition to improving the flexibility of these algorithms, Mothur has added a number of other features including calculators and visualisation tools.

Mothur is available as a module on Apocrita.


To run the latest installed version of Mothur, simply load the mothur module:

module load mothur

then run one of the appname commands such as

mothur inputfile.mothur

Multiple-processor Commands

The following mothur commands can take advantage of multiple processors:

align.seqs chimera.bellerphon chimera.ccode chimera.check
chimera.pintail chimera.slayer chimera.uchime classify.seqs
cluster.split dist.seqs dist.shared filter.seqs
indicator metastats pairwise.seqs parsimony
phylo.diversity rarefaction.single screen.seqs summary.seqs
summary.shared trim.seqs unifrac.unweighted unifrac.weighted

To specify that multiple processors can be used, add the processors option to a command. Once a mothur command has had the processors option set, subsequent commands that allow the processors option will use the value originally specified:

mothur > filter.seqs(fasta=gg_13_5_99.align, trump=., processors=4)

Example jobs

Serial job

Here is an example job running on 12 cores:

#$ -cwd
#$ -j y
#$ -pe smp 12
#$ -l h_rt=4:0:0
#$ -l h_vmem=2G

module load mothur
mothur inputfile.mothur