WGASA can efficiently align large (e.g. bacterial) genomes. In addition, the developers have created a parallel version that runs in minutes, allowing the SAP simulations, involving thousands of calls to WGASA, to complete in a feasible time frame. In addition to the SAP analyses, this tool has enabled us to revisit signature predictions for several important organisms, such as the food-borne pathogen Listeria, that were previously problematic because some of the sequences were available only in draft format.