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. 

This requires argtable.