Using muscle to produce multiple sequence alignments in

Producing high-quality multiple sequence alignments of DNA, RNA, or amino acid sequences is often an essential component of any comparative sequence-based study. The MUSCLE algorithm employs a progressive alignment approach to optimise pairwise alignment scores, and achieves both high accuracy and reduced computational time even when handling thousands of sequences (Edgar, 2004,a). The R package muscle integrates the MUSCLE algorithm into the Bioconductor project by utilizing existing Biostrings classes for representing sequence objects and multiple alignments