Software
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 ClustalW and T-coffee for alignment, and BLAST and FASTA3x for database searching.
Alignment algorithms and software can be directly compared to one another using a standardized set of benchmark reference multiple sequence alignments known as BAliBASE. The data set consists of structural alignments, which can be considered a standard against which purely sequence-based methods are compared. The relative performance of many common alignment methods on frequently encountered alignment problems has been tabulated and selected results published online at BAliBASE. A comprehensive list of BAliBASE scores for many (currently 12) different alignment tools can be computed within the protein workbench STRAP.
Read more about this topic: Sequence Alignment