MUSCLE is a program for generating multiple alignments of amino acid and nucleotide sequences. The speed and accuracy of MUSCLE were compared with T-Coffee, MAFFT, and CLUSTALW and achieved the highest or joint highest rank in accuracy in all tests. When used without refinement its accuracy is the same as T-Coffee or MAFFT and is the fastest at aligning large sequences of the three.
To learn about MUSCLE please read this paper:
Edgar, Robert C. (2004), MUSCLE: multiple sequence alignment with high accuracy and high throughput, Nucleic Acids Research 32(5), 1792-97
To Read Online(http://nar.oxfordjournals.org/cgi/content/full/32/5/1792?ijkey=48Nmt1tta0fMg&keytype=ref)