Horizontal gene transfers (HGT) have played a significant role in prokaryotic genome evolution, and the genes constituting a prokaryotic genome appear to be divided into two classes: a "core gene pool" that comprises intrinsic genes encoding the proteins of basic cellular functions, and a "flexible gene pool" that comprises HGT-acquired genes encoding proteins which function under particular conditions, such as genomic islands. Therefore, the identification of the set of intrinsically conserved genes, or the genomic core, among a taxonomic group is crucial not only for establishing the identity of each taxonomic group, but also for understanding prokaryotic diversity and evolution.

We have developed a method, named CoreAligner, for identifying the core structure of related genomes, which is defined as a set of sufficiently long segments in which gene orders are conserved among multiple genomes so that they are likely to have been inherited mainly through vertical transfer. Using a dynamic programming based algorithm, CoreAligner finds the order of pre-identified orthologous groups (OGs) that retains to the greatest possible extent the conserved gene orders.