Mothur is an open source software package for bioinformatics data processing. The package is frequently used in the analysis of DNA from uncultured microbes.

Detailed information about Mothur can be found here:


  • 1.46.0

  • 1.47.0

  • 1.48.0


  • mothur


You can load the modules by:

module load biocontainers
module load mothur/1.47.0

Interactive job

To run mothur interactively on our clusters:

(base) UserID@bell-fe00:~ $ sinteractive -N1 -n12 -t4:00:00 -A myallocation
salloc: Granted job allocation 12345869
salloc: Waiting for resource configuration
salloc: Nodes bell-a008 are ready for job
(base) UserID@bell-a008:~ $ module load biocontainers mothur/1.47.0
(base) UserID@bell-a008:~ $ mothur
Linux version

Using ReadLine,Boost,HDF5,GSL
mothur v.1.47.0
Last updated: 1/21/22
Patrick D. Schloss

Department of Microbiology & Immunology

University of Michigan

When using, please cite:
Schloss, P.D., et al., Introducing mothur: Open-source, platform-independent, community-supported software for describing and comparing microbial communities. Appl Environ Microbiol, 2009. 75(23):7537-41.

Distributed under the GNU General Public License

Type 'help()' for information on the commands that are available

For questions and analysis support, please visit our forum at

Type 'quit()' to exit program

[NOTE]: Setting random seed to 19760620.

Interactive Mode

mothur > align.seqs(help)
mothur > quit()

Batch job


Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To submit a sbatch job on our clusters:

#SBATCH -A myallocation     # Allocation name
#SBATCH -t 10:00:00
#SBATCH -n 24
#SBATCH --job-name=mothur
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers mothur/1.47.0

mothur batch_file