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-appsmodule.
Usage
MUSCLE is part of the bio-apps collection on Roihu. Load the bio-apps module tree and then the MUSCLE module:
Align sequences from a FASTA file:
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.