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Multiple alignment program for amino acid or nucleotide sequences.

MAFFT is available as a module on Apocrita.


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:

#$ -cwd
#$ -j y
#$ -pe smp 2
#$ -l h_rt=1:0:0
#$ -l h_vmem=1G

module load mafft

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