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.

• Clustal Omega
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• Clustal Omega home page

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