Applications/Mafft

Application Details

• Description: MAFFT is used to create multiple sequence alignments of amino acid or nucleotide sequences.
• Version: 2.2.9 (compiled with gcc)
• Modules: mafft/7.397
• Licence: Open source (Github)

Usage Examples

Manual execution

[username@login01 ~]$ module add mafft/7.397
[username@login01 ~]$ mafft

---------------------------------------------------------------------

   MAFFT v7.397 (2018/Apr/16)

        MBE 30:772-780 (2013), NAR 30:3059-3066 (2002)
        https://mafft.cbrc.jp/alignment/software/
---------------------------------------------------------------------


Input file? (fasta format)
@

Command line processing

[username@login01 ~]$ module add mafft/7.397
[username@login01 ~]$ mafft [arguments] input > output

An alias for an accurate option (L-INS-i) for an alignment of up to ∼200 sequences × ∼2,000 sites:

[username@login01 ~]$ mafft-linsi input > output

A fast option (FFT-NS-2) for a larger sequence alignment:

[username@login01 ~]$ mafft input > output

If not sure which option to use,

[username@login01 ~]$ mafft --auto input > output

Batch Job

#SBATCH J mafftjob
#SBATCH N 1
#SBATCH --exclusive
#SBATCH --cpus-per-task=4
#SBATCH -o %N-%j.out
#SBATCH -e %N-%j.err

module purge
module load mafft/7.397

mafft --thread $SLURM_CPUS_PER_TASK ex1 > outfile

Further Information

• https://mafft.cbrc.jp/alignment/software/
• https://en.wikipedia.org/wiki/MAFFT

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