Applications/Mafft
From HPC
Contents
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
#!/bin/bash #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