Mbs: Modifying Hudson's ms software to generate samples of DNA sequences with a biallelic site under selection

Abstract

Background: The pattern of single nucleotide polymorphisms, or SNPs, contains a tremendous amount of information with respect to the mechanisms of the micro-evolutionary process of a species. The inference of the roles of these mechanisms, including natural selection, relies heavily on computer simulations. A coalescent simulation is extremely powerful in generating a large number of samples of DNA sequences from a population (species) when all mutations are neutral, and Hudson's ms software is frequently used for this purpose. However, it has been difficult to incorporate natural selection into the coalescent framework. Results: We herein present a software applicationto generate samples of DNA sequences when there is a biallelic site targeted by selection. This software application, referred to as mbs, is developed by modifying Hudson's ms. The mbs software is so flexible that it can incorporate any arbitrary histories of population size changes and any mode of selection as long as selection is operating on a biallelic site. Conclusion: mbs provides opportunities to investigate the effect of any mode of selection on the pattern of SNPs under various demography. © 2009 Teshima and Innan; licensee BioMed Central Ltd.