Clustal W algorithm for multiple sequence alignment revisited

Multiple sequence alignment is one of the most important problems arising in DNA and protein recognition. Clustal W is a well known and practically [ applied method used for solving the problem. In the paper, a modification of the algorithm is described which shortens considerably its mean running time. The modification uses graphs of partial alignments and operations on resulting semi-cliques. As shown by an extensive computational experiment running time is reduced up to 50%, as compared with the original approach.