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.

• ClustalW
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

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

• ClustalW at EBI

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