A more complete list of available software categorized by algorithm and alignment type is available at sequence alignment software, but common software tools used for general sequence alignment tasks include ClustalW2 and T-coffeeT-coffee for alignment, and BLAST and FASTA3x for database searching. Commercial tools such as DNASTAR Lasergene, Geneious, and PatternHunter are also available. Tools annotated as performing sequence alignment are listed in the bio.tools registry.
