Clustal is a widely used, multiple sequence alignment program. This is Clustal Omega, the latest addition to the Clustal family. It offers a significant increase in scalability over previous versions, allowing hundreds of thousands of sequences to be aligned in only a few hours. In addition, the quality of alignments is superior to previous versions, as measured by a range of popular benchmarks. Clustal Omega is currently a command line-only tool, and is only suitable for aligning protein sequences, not DNA or RNA. If you like Clustal-Omega please cite: Sievers F, Wilm A, Dineen D, Gibson TJ, Karplus K, Li W, Lopez R, McWilliam H, Remmert M, Söding J, Thompson JD, Higgins DG. Fast, scalable generation of high-quality protein multiple sequence alignments using Clustal Omega. Mol Syst Biol. 2011 Oct 11;7:539. doi: 10.1038/msb.2011.75. PMID: 21988835. This requires argtable.