From the MUSCLE web site: MUSCLE is one of the best-performing multiple alignment programs according to published benchmark tests, with accuracy and speed that are consistently better than CLUSTALW. MUSCLE can align hundreds of sequences in seconds. Most users learn everything they need to know about MUSCLE in a few minutes—only a handful of command-line options are needed to perform common alignment tasks.


  • 3.8.31

Authorized Users

  • CIRCE account holders
  • SC account holders


  • CIRCE cluster
  • SC cluster


MUSCLE requires the following module file to run:

  • apps/muscle/3.8.31


The MUSCLE user guide is essential to understanding the application and making the most of it. The guide and this page should help you to get started with your simulations. Please refer to the Documentation section for a link to the guide.

  • Note on CIRCE: Make sure to run your jobs from your $WORK directory!
  • Note: Scripts are provided as examples only. Your SLURM executables, tools, and options may vary from the example below. For help on submitting jobs to the queue, see our SLURM User’s Guide.

Using MUSCLE on the command line

Once connected to CIRCE/SC, you can open MUSCLE using the steps below:

[user@login0 ~]$ module add apps/muscle/3.8.31
[user@login0 ~]$ muscle 


Home Page, User Guides, and Manuals

Reporting Bugs

Report bugs with MUSCLE to the IT Help Desk: