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Warning!

Puhti and Mahti computing services have been decommissioned and no new jobs are accepted or executed on its compute nodes. Puhti and Mahti login nodes and storage services are planned to remain available until 15 October 2026. Clean up unnecessary files and move any data you need to keep by 31 August 2026. See the Roihu data migration guide for instructions on transferring your data to Roihu.

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.

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