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.

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

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

• MUSCLE home page

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