MUSCLE: multiple sequence alignment with improved accuracy and speed

We present MUSCLE, a new program for creating multiple alignments of protein sequences. MUSCLE achieves the highest scores so far reported on four alignment benchmarks: Balibase, PREFAB, SABmark and SMART, achieving accuracy from 1% to 2.5% higher than T-Coffee and execution times that are generally lower than CLUSTALW for typical input data. With options designed for high-throughput applications, MUSCLE gives average accuracy statistically indistinguishable from T-Coffee and is the fastest published method for large numbers of sequences, able to align 5,000 sequences of length 300 in 7 minutes on a desktop computer. MUSCLE is freely available at http://www.drive5.com/muscle.