MUSCLE

Category(ies): Bioinformatics

Author / Distributor:
Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97.

Description:

MUSCLE is public domain multiple alignment software for protein and nucleotide sequences. MUSCLE stands for multiple sequence comparison by log-expectation.

altix: running program | Documentation | Installation | System

Running Program:

muscle -in seqs.fa -out seqs.afa

where seqs.fa as input sequence file and seqs.afa as output. The sample file can be copied at

cp /usr/local/src/muscle/muscle3.6/seqs.fa seqs.fa

Documentation: http://www.drive5.com/muscle/muscle.html

Installation:

Source code downloaded from http://www.drive5.com/muscle/downloads.htm
Compiled by gcc

System(s): Unix

inQuiry: not available at inQuiry

pcluster: Not available on pcluster

rcluster,IOB: running program | Documentation | Installation | System

Running Program: also refer to submit jobs to queues at rcluster,IOB

Submit jobs to the queue:
Firstly, create a muscle.sub.sh file with contents as below. The working_directory is the path to your working directory (e.g., it could be /home/labname/username/subdir or /scratch/username/subdir ). You can add other parameters after muscle commands.
Please refer to running jobs in the queue for details

#!/bin/csh
cd working_directory
time muscle -in seqs.fa -out seqs.afa > muscle.out

chmod u+x muscle.sub.sh

bsub -q queueName -o seqs.%J.out -e seqs.%J.err ./muscle.sub.sh

where seqs.fa as input sequence file and seqs.afa as output. The sample file can be copied at

cp /usr/local/src/muscle/muscle3.6/seqs.fa seqs.fa

Use following command to check if your jobs are done:

bjobs -u my-user-name

Documentation: Same as altix

Installation: Same as altix

System(s): Unix