MAFFT

Multiple alignment program for amino acid or nucleotide sequences.

MAFFT is available as a module on Apocrita.

Usage

To run the default installed version of MAFFT, simply load the mafft module:

module load mafft

For usage documentation, run mafft --help.

Example job

Serial job

Here is an example job running on 2 cores and 2GB of memory:

#!/bin/bash
#SBATCH --ntasks=2        # (or -n 2) Request 2 cores
#SBATCH --mem-per-cpu=1G  # Request 1GB RAM per core (2GB total)
#SBATCH --time=1:0:0      # (or -t 1:0:0) Request 1 hour runtime

module load mafft

mafft --thread ${SLURM_NTASKS} \
      input > output

References

• MAFFT website
• MAFFT manual