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-appsmodule.
Usage
MAFFT is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MAFFT module:
A basic automatic alignment (MAFFT chooses the strategy based on the data size):
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.