We present some experiences with the problem of multiple genome comparison, analogous to multiple sequence alignment in sequence comparison, under the inversion and transposition distance metrics, given a fixed phylogeny. We first describe a heuristic for the case in which phylogeny is a star on three vertices and then use this to approximate the multiple genome comparison problem via local search.
Mitochondrial Genome Rearrangements in Glomus Species Triggered by Homologous Recombination between Distinct mtDNA Haplotypes