DIALIGN 2: improvement of the segment-to-segment approach to multiple sequence alignment

Motivation: The performance and time complexity of an improved version of t he segment-to-segment approach to multiple sequence alignment is discussed. In this approach, alignments are composed from gap-free segment pairs, and the score of an alignment is defined as the sum of so-called weights of th ese segment pairs. Results: A modification of the weight function used in the original version of the alignment program DIALIGN has two important advantages: it can be a pplied to both globally and locally related sequence sets, and the running time of the program is considerably improved The time complexity of the alg orithm is discussed theoretically, and the program running time is reported for various test examples.