MUSCLE

Overview

MUSCLE, or MUltiple Sequence Comparison by Log-Expectation,
is used for multiple sequence alignment of input sequences using the amino acid alphabet.

Availability

Cluster	Module/Version
BOSE	muscle/5.3
BGSC	Not Available

Note: You can simply use module load muscle to activate the most recently installed version of this software.

Arguments / Options

This is a list of arguments for the muscle command that we wanted to highlight. Use this online man page for a full list.

Option	Description
-align	Align FASTA input
-super5	Align sequences using the Super5 algorithm
-efastats	Reports miscellaneous information about the MSAs stored in ensemble FASTA (EFA) format
-fa2efa	Creates one ensemble FASTA (EFA) file from one or more FASTA files
-disperse	Calculates the dispersion of an ensemble
-letterconf	Calculates letter confidence values. Outputs FASTA format, with letters replaced by confidence, 0-9
-maxcc	Extract the MSA with highest column confidence from an ensemble
-resample	Creates a resampled ensemble from an existing ensemble (usually a diversified ensemble)

Sample Slurm Script

submit.sh

#!/bin/bash
# -- SLURM SETTINGS -- #
# [..] other settings here [..]

# The following settings are for the overall request to Slurm
#SBATCH --ntasks-per-node=32     # How many CPU cores do you want to request
#SBATCH --nodes=1                # How many nodes do you want to request

# -- SCRIPT COMMANDS -- #

# Load the needed modules
module load muscle                         # Load MUSCLE
muscle -align seqs.fa -output aln.afa      # Run MUSCLE

Real Example

Has your research group used MUSCLE in a project? Contact the HPC Team and we'd be glad to feature your work.

Citation

Please include the following citation in your papers to support continued development of MUSCLE.

Edgar, RC (2021), MUSCLE v5 enables improved estimates of phylogenetic tree confidence by ensemble bootstrapping, bioRxiv 2021.06.20.449169. https://doi.org/10.1101/2021.06.20.449169.