The applications listed here are available for use in the Discovery Environment and are documented in: Discovery Environment Manual.

Discovery Environment Applications List

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MUSCLE performs DNA or amino acid multiple sequence alignment.

MUSCLE stands for MUltiple Sequence Comparison by Log- Expectation. MUSCLE may achieve both better average accuracy and better speed than ClustalW2 or T-Coffee, depending on the chosen options.


This documentation corresponds to the DE app named "MUSCLE-hpc-3.8.31", which runs on the Stampede supercomputer. See MUSCLE for documentation of the app "Muscle-3.8.31", which runs on the UA HTCondor cluster. These two apps can be used interchangeably.  Wait times may be shorter for Muscle-3.8.31.

Quick Start

  • To use MUSCLE, upload your data in FASTA format.
  • Resources: documentation

Test Data

All files are located in the Community Data directory of the iPlant Discovery Environment at the following path:

Community Data > iplantcollaborative > example_data > muscle-3.8.31

Input File(s)

  •  Use muscle_in.fa (FASTA file) as a test input file.
  • MUSCLE takes only FASTA files as input. 
  • MUSCLE allows lines of any length in a FASTA file. (Some programs limit lines to e.g., 80 characters).
  • MUSCLE does not support comments in FASTA files.
  • White space characters (blanks and tabs) are discarded if found in sequence data, but many other tools do not allow this and the practice is not recommended.

Parameters Used in App

When the app is run in the Discovery Environment, use the following parameters with the above input file(s) to get the output provided in the next section below

  • output format: Leave as default format (FASTA)
  • output name: Leave as default name (aligned.fa)

For information on adding command line parameters, please see the MUSCLE documentation:

Output File(s)

  • MUSCLE generates multiple sequence alignments in a variety of output formats.
  • If you used the input and parameters suggested in this example, you should get the follow as output:
    • aligned.fa

Tool Source for App


MUSCLE v3.8.31 by Robert C. Edgar

Please cite:

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput
  Nucleic Acids Res. 32(5):1792-1797 [Link to PubMed].

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity
  BMC Bioinformatics, (5) 113 [Link to PubMed].