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.

Clustal Omega

Clustal Omega is a fast and scalable program for multiple sequence alignment of protein and nucleotide sequences. It can align large numbers of sequences and produce high-quality alignments.

License

Free to use and open source under GNU GPLv2.

Available

  • Roihu: 1.2.4, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load clustal-omega/1.2.4

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

clustalo -i sequences.fasta -o aligned.fasta --threads 4

Example batch script

#!/bin/bash
#SBATCH --job-name=clustalo
#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=4
#SBATCH --mem-per-cpu=2G

module load bio-apps/v202603
module load clustal-omega/1.2.4

clustalo -i sequences.fasta -o aligned.fasta --threads $SLURM_CPUS_PER_TASK

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