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Complex strategies have been developed for whole genome alignment of multiple species. In the case of population genomics studies, the sequences being aligned are often very similar. We propose a reference coordinate system that simplifies the task of comparing many closely related genomes while taking into account structural rearrangements. We implemented software to compare a group of three strains of the malaria mosquito, Anopheles gambiae and a group of three strains of the malaria parasite, Plasmodium falciparum. Our simplified representation enables us to leverage existing work on the species while performing fine-grained analysis on the new draft genomes. Further, this approach will easily scale to hundreds of closely related genomes, enabling new analyses in population genomics as additional genomic sequences become available. [ABSTRACT FROM AUTHOR]