Motivation: DCA is a new computer program for multiple sequence alignment which utilizes a 'divide-and-conquer' type of heuristic approach. We present a new computer program, DCA, for the multiple alignment of DNA, RNA and protein sequences. Utilizinga divide-and-conquer type heuristic (cf. Brinkmann et al., 1997), it aims to produce multiple alignments which minimize the sum-of-pairs alignment score. Consequently, and in contrast to most other multiple sequence alignment programs currently in use which construct alignments by progressively aligning alignments of alignments of alignments (see, for instance, Barton and Sternberg, 1987; Thompson et al., 1994; Gotoh, 1995; Feng and Doolittle, 1996), DCA processes any given sequence family simultaneously, already taking all sequences into consideration at its first alignment step.
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