Genomes are clearly suited for inferring common ancestry and for understanding ancestor–descendent relationships and interspecies gene transfer. Genomic evolutionary models can tell us a great deal about the processes that drive genome evolution, the mutational and selective pressures that lead to the genesis of biochemical pathways and operons, and the nature and extent of lateral gene transfer (LGT). Simultaneously, a robust phylogeny can be constructed that depicts the evolutionary relationships of the organisms in which the genomes are found. Several approaches have been employed to infer species phylogenies at the genome level. In general terms, these can be divided into ad hoc summary statistics based on genome content, the use of concatenated alignments and the use of consensus methods (i.e. phylogenetic supertrees [1])