MAFFT

MAFFT is a multiple sequence alignment program for unix-like operating systems. It offers a range of alignment strategies, from fast progressive methods for large numbers of sequences to accurate iterative-refinement methods for smaller datasets.

• MAFFT
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source under the BSD license.

Available

• Roihu: 7.525, via the bio-apps module.

Usage

MAFFT is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MAFFT module:

module load bio-apps/v202603
module load mafft/7.525

A basic automatic alignment (MAFFT chooses the strategy based on the data size):

mafft --auto --thread 8 input.fasta > aligned.fasta

Example batch script

#!/bin/bash
#SBATCH --job-name=mafft
#SBATCH --account=<project>
#SBATCH --output=output_%j.txt
#SBATCH --error=errors_%j.txt
#SBATCH --partition=small
#SBATCH --time=04:00:00
#SBATCH --nodes=1
#SBATCH --ntasks=1
#SBATCH --cpus-per-task=8
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load mafft/7.525

mafft --auto --thread $SLURM_CPUS_PER_TASK input.fasta > aligned.fasta

Replace <project> with your CSC project (for example project_2001234).

See creating a batch job script for Roihu for more information about running batch jobs.

Support

CSC Service Desk

More information

• MAFFT home page

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