Documentation
 

 
Manuals
User guide as PDF file
User guide as web page

Papers
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.
doi:10.1093/nar/gkh340

Edgar, R.C. (2004) MUSCLE: a multiple sequence alignment method with reduced time and space complexity BMC Bioinformatics, (5) 113.
doi:10.1186/1471-2105-5-113
 

 
News
USEARCH and UCLUST released. Search and clustering hundreds of times faster than BLAST.
MUSCLE v3.8 released.
 
Blog
Multiple protein alignment is dead
Big alignments -- do they make sense?