MUSCLE is multiple alignment software.


  • MUSCLE web home
  • Citations:  If you use MUSCLE, please cite these papers.The Nucleic Acids Research paper is the primary citation.  The BMC Bioinformatics paper gives more technical details.

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]. 



To see what versions of MUSCLE are available type

module avail muscle

To see what other modules are needed, what commands are available and how to get additional help type

module help muscle

To use MUSCLE, include a command like this in your batch script or interactive session to load the muscle module:

module load muscle

Be sure you also load any other modules needed, as listed by the module help muscle command.