Summary: A Fast Algorithm for the Optimal Alignment of Three Strings.
Department of Computer Science,
Partly supported by an Australian Research Council grant.
J. Theor. Biol. 164(2) 261269 Sept 1993
Fast Algorithm for Alignment of Three Strings. 2
Abstract. Ukkonen's (pairwise) string alignment technique is extended to the problem of finding an
optimal alignment for three strings. The resulting algorithm has worstcase timecomplexity O(nd 2 ) and
spacecomplexity O(d 3 ), where the string lengths are ”n and d is the threeway editdistance based on tree
costs. In practice the algorithm usually runs in O(n+d 3 ) time. The algorithm is particularly fast when the
strings are similar in which case d<
Threeway alignment is an important special case in string alignment. Each internal node in an
unrooted, binary evolutionarytree has three neighbours. The algorithm presented can be used as an
iterative step in a heuristic multiplealignment program for more than three strings.
Keywords: alignment, editdistance, multiplealignment, sequence, string, three.