Muscle

Introduction

Muscle is a modified progressive alignment algorithm which has comparable accuracy to MAFFT, but faster performance.

For more information, please check its website: https://biocontainers.pro/tools/muscle and its home page: http://www.drive5.com/muscle/muscle_userguide3.8.html.

Versions

  • 3.8.1551

  • 5.1

Versions

  • 3.8.1551

  • 5.1

Commands

  • muscle

Module

You can load the modules by:

module load biocontainers
module load muscle

Example job

Warning

Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.

To run Muscle on our clusters:

#!/bin/bash
#SBATCH -A myallocation     # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=muscle
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out

module --force purge
ml biocontainers muscle

muscle -align seqs2.fasta  -output seqs.afa