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-3.8.31", which runs on the UA HTCondor cluster. See MUSCLE-3.8.31 on Stampede for documentation of the app "MUSCLE-hpc-3.8.31", which runs on the Stampede supercomputer.  These two apps run the same executable and can be used interchangeably.  Wait 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)

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.

Either leave only "Default parameters..." OR delete the "Default parameters..." line and fill in the "Use these parameters..." section. Then, delete this box.

  • Default parameters only, no further configuration needed.


  • Use these parameters within the DE app interface:
    • parameter name - value/setting
    • parameter name - value/setting

Output File(s)

  • Generates multiple sequence alignments in a variety of output. This output example may be used as input to phyml: example_out.phylip

Tool Source for App

Basic Help

MUSCLE v3.8.31 by Robert C. Edgar
This software is donated to the public domain.
Please cite: Edgar, R.C. Nucleic Acids Res 32(5), 1792-97.