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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