MUSCLE5

MUSCLE5 is the current major version of MUSCLE, widely-used software for making multiple alignments of protein and nucleotide sequences. It introduces new algorithms and the ability to generate ensembles of alternative alignments. For the older version 3, see MUSCLE.

• MUSCLE5
  • License
  • Available
  • Usage
    • Example batch script
  • Support
  • More information

License

Free to use and open source under GNU GPLv3.

Available

• Roihu: 5.1.0, via the bio-apps module.

Usage

MUSCLE5 is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MUSCLE5 module:

module load bio-apps/v202603
module load muscle5/5.1.0

Align sequences from a FASTA file:

muscle5 -align sequences.fasta -output aligned.fasta -threads 8

Example batch script

#!/bin/bash
#SBATCH --job-name=muscle5
#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=8
#SBATCH --mem-per-cpu=4G

module load bio-apps/v202603
module load muscle5/5.1.0

muscle5 -align sequences.fasta -output 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

• MUSCLE5 home page
• MUSCLE5 GitHub repository

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