Abstract
During evolution the gene order in a genome is generally not well conserved because it is subject to be changed by genome rearrangements, such as reversals, transpositions, fusions, fissions and translocations. The studies for analyzing the differences between the gene orders of a set of species genomes have been increasingly recognized as a powerful tool in phylogenetic tree reconstruction, as they can help biologists to gain a better understanding of the evolution of several groups of genomes. In this chapter, we shall introduce our web server, called SoRT2, which allows the user to perform genome rearrangement analysis involving reversals, generalized transpositions and translocations (including fusions and fissions), and also infer phylogenetic trees of genomes being considered based on their pairwise genome rearrangement distances. In addition, we shall demonstrate its SoRT2 in reconstruction of phylogenetic trees by using some simulated datasets, as well as three biological datasets of gene orderings from mitochondrial, mammalian and bacterial genomes, respectively.