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.

MUSCLE

MUSCLE is a widely-used program for creating multiple sequence alignments of protein and nucleotide sequences. This is MUSCLE version 3; for the current major version see MUSCLE5.

License

MUSCLE is free to use and in the public domain. See the MUSCLE home page.

Available

  • Roihu: 3.8.31, via the bio-apps module.

Usage

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

module load bio-apps/v202603
module load muscle/3.8.31

Align sequences from a FASTA file:

muscle -in sequences.fasta -out aligned.fasta

Example batch script

#!/bin/bash
#SBATCH --job-name=muscle
#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 muscle/3.8.31

muscle -in sequences.fasta -out 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.

Support

CSC Service Desk

More information