Software Category


Mauve is one of the bioinformatics programs available on RCC Systems. It is a genomic sequence alignment program designed to align multiple genomic sequences when there are large-scale evolutionary events that need to also be considered when computing said alignments. These events can include such things as rearrangement and inversion among others.

Using Mauve on RCC Resources

Before running Mauve, you need to load the gnu module:

module load gnu

Mauve Command Line Tools in Serial

Mauve also has two command line tools mauveAligner and progressiveMauve both of which are sequence alignment tools. These can be run in serial using the commands:

mauveAligner TEST1.seq

In the above example, TEST.seq is a genomic sequence file which can be in one of three formats as stated on the Mauve website (Fasta, Multi Fasta or GenBank). Note that you can have more than one sequence file in the command line arguments. See Mauve Aligner documentation for more information.

Mauve Command Line Tools in Parallel

To speed up alignments, Mauve can be run in parallel using the GNU OpenMPI module which can be loaded by typing module load gnu openmpi.

A Slurm script can be written to do this as well. For example, using 4 processors again, we could write a script like:


#SBATCH -J Mauve_Test
#SBATCH -n 4
#SBATCH -p genacc_q
#SBATCH -t 00:10:00
#SBATCH --mail-type=ALL

module load gnu openmpi
mpirun -np 4 mauveAligner TEST.seq