Computational Tools for the Analysis of Rearrangements in Mammalian Genomes

The chromosomes of mammalian genomes exhibit reasonably high levels of similarity that can be used to study small-scale sequence variations. A different approach is to study the evolutionary history of rearrangements in entire genomes based on the analysis of gene or segment orders. This chapter describes three computational tools (GRIMM-Synteny, GRIMM, and MGR) that can be used separately or in succession to contrast different organisms at the genome-level to exploit large-scale rearrangements as a phylogenetic character.