Computational methods for the analysis of mitochondrial genome rearrangements

The evolution of gene orders by genome rearrangements is an important source of phylogenetic information. A large number of mitochondrial gene orders is nowadays available for phylogenetic analyses. On the one hand their small size and nearly perfectly conserved gene content makes them suitable for many approaches. But the different types of relevant rearrangement operations, on the other hand, complicate the analysis. In this chapter we review approaches for genome rearrangement analysis suitable for mitochondrial gene orders. This includes the analysis of pairs of gene orders as well as of larger sets of gene orders with and without a given phylogenetic tree. Particular attention is payed to the analysis of the tandem duplication random loss rearrangement