Skip to content

Docs CSC now features an automatic Finnish translation. Click here for more information.

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.

ClustalW

ClustalW is a classic program for the multiple alignment of nucleic acid and protein sequences. For large-scale alignments, consider the faster Clustal Omega.

License

Free to use and open source under GNU LGPLv3.

Available

  • Roihu: 2.1, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load clustalw/2.1

The program is run with the clustalw2 command. For example, to align sequences in a file:

clustalw2 -infile=sequences.fasta -outfile=aligned.aln

Example batch script

#!/bin/bash
#SBATCH --job-name=clustalw
#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=1
#SBATCH --mem=4G

module load bio-apps/v202603
module load clustalw/2.1

clustalw2 -infile=sequences.fasta -outfile=aligned.aln

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