MUSCLE There are two papers. The first (NAR) introduced the algorithm, and is the primary citation if you use the program. The second (BMC Bioinformatics) gives more technical details, including descriptions of non-default options. 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 ].