Fast Sorting by Reversal

Analysis of genomes evolving by inversions leads to a combinatorial problem of sorting by reversals studied in detail recently. Following a series of work recently, Hannenhalli and Pevzner developed the rst polynomial algorithm for the problem of sorting signed permutations by reversals and proposed an O(n 4) implementation of the algorithm. In this paper we exploit a few combinatorial properties of the cycle graph of a permutation and propose an O(n 2 (n)) implementation of the algorithm where is the inverse Ackerman function. Besides making this algorithm practical, our technique improves implementations of the other rearrangement distance problems.