Teshima Kosuke M, Innan Hideki
Hayama Center for Advanced Studies, Graduate University for Advanced Studies, Hayama, Kanagawa 240-0193, Japan.
BMC Bioinformatics. 2009 May 30;10:166. doi: 10.1186/1471-2105-10-166.
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.
We herein present a software application to 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.
mbs provides opportunities to investigate the effect of any mode of selection on the pattern of SNPs under various demography.
单核苷酸多态性（SNP）模式包含了有关物种微观进化过程机制的大量信息。对包括自然选择在内的这些机制作用的推断在很大程度上依赖于计算机模拟。当所有突变都是中性时，合并模拟在从一个种群（物种）生成大量DNA序列样本方面极其强大，并且Hudson的ms软件经常用于此目的。然而，将自然选择纳入合并框架一直很困难。
我们在此展示了一个软件应用程序，用于在存在受选择靶向的双等位基因位点时生成DNA序列样本。这个软件应用程序称为mbs，是通过修改Hudson的ms开发的。mbs软件非常灵活，只要选择作用于双等位基因位点，它就可以纳入任何任意的种群大小变化历史和任何选择模式。
mbs为研究各种人口统计学下任何选择模式对SNP模式的影响提供了机会。
