AbstractWe give two parallel algorithms for sequence comparison on the Connection Machine 2 (CM‐2). The specific comparison measure we compute is theedit distance: given a finite alphabet ∑ and two input sequencesXϵ ∑+andYϵ ∑+the edit distanced(X,Y)is the minimum cost of transformingXintoYvia a series of weighted insertions, deletions and substitutions of characters. The edit distance comparison measure is equivalent to or subsumes a broad range of well known sequence comparison measures.The CM‐2 is very fast at performing parallel prefix operations. Our contribution consists of casting the problem in terms of these operations. Our first algorithm computesd(X,Y)usingNprocessors andO(M S)time units, whereM= min(|X|,||Y|) + 1,N= max(|X|,|Y|) + 1 andSis the time required for a parallel prefix operation. The second algorithm computesd(X,Y)usingNMprocessors andO((logNlogM)(S+R)) time units, whereRis the time for a ‘router’ communication step—one in which each processor is able to read data, in parallel, from the memory of any other processor. Our algorithms can also be applied to several variants of the problem, such as subsequence comparisons, and one—many and many‐many comparisons on 'sequence databases'.