MUSCLE manual
Papers and citing MUSCLE
There are two papers. The first paper introduced the program and described some initial validation. This paper also introduced the PREFAB benchmark, which was the first published alternative to BALIBASE. The second paper is a detailed description of the algorithm and its motivation, including several non-default options. The preferred citation for use of the program is the first (Nucleic Acids Res.). 

Edgar, R.C. (2004) MUSCLE: multiple sequence alignment with high accuracy and high throughput.Nucleic Acids Res. 32(5):1792-1797.

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113.