Clustal (Thompson et al., 1994) is a commonly used alignment program that will handle protein, DNA, or RNA sequence data and is actively maintained (http://www.clustal.org/). The version ClustalW, currently in version 2.1 (Larkin et al., 2007), can be installed locally and run in command-line or it can be run remotely at an off-site server where it is already installed (i.e. at EMBL-EBI; http://www.ebi.ac.uk/Tools/msa/clustalw2/ or at GenomeNet; http://www.genome.jp/tools/clustalw/). ClustalW allows the user to specify certain parameters of the alignment algorithm. Users who do not have the knowledge to make parameter specifications may choose general purpose, default settings (as at the EMBL-EBI site). ClustalX, a graphical version and Clustal Omega, specifically for large sets of protein sequence data are also available.