To cite the 'muscle' package in publications use:

  Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high
  accuracy and high throughput. Nucleic Acids Res 32:1792-1797.
  
  doi:10.1093/nar/gkh340

A BibTeX entry for LaTeX users is

  @Article{,
    title = {MUSCLE: multiple sequence alignment with high accuracy and high throughput},
    author = {Robert C. Edgar},
    year = {2004},
    journal = {Nucleic Acids Res},
    volume = {32},
    pages = {1792-1797},
    doi = {10.1093/nar/gkh340},
  }