EnviroSPACE laboratory, Climate Change and Climate Impacts, Institute for Environmental Sciences, University of Geneva, Battelle - Building D, 7 route de Drize, 1227 Carouge, Switzerland.
Bioinformatics. 2010 Dec 1;26(23):2993-4. doi: 10.1093/bioinformatics/btq579. Epub 2010 Oct 17.
SPLATCHE2 is a program to simulate the demography of populations and the resulting molecular diversity for a wide range of evolutionary scenarios. The spatially explicit simulation framework can account for environmental heterogeneity and fluctuations, and it can manage multiple population sources. A coalescent-based approach is used to generate genetic markers mostly used in population genetics studies (DNA sequences, SNPs, STRs or RFLPs). Various combinations of independent, fully or partially linked genetic markers can be produced under a recombination model based on the ancestral recombination graph. Competition between two populations (or species) can also be simulated with user-defined levels of admixture between the two populations. SPLATCHE2 may be used to generate the expected genetic diversity under complex demographic scenarios and can thus serve to test null hypotheses. For model parameter estimation, SPLATCHE2 can easily be integrated into an Approximate Bayesian Computation (ABC) framework.
SPLATCHE2 is a C++ program compiled for Windows and Linux platforms. It is freely available at www.splatche.com, together with its related documentation and example data.
SPLATCHE2 是一个程序，用于模拟广泛进化情景下的种群动态和由此产生的分子多样性。这个具有空间显式的模拟框架可以考虑环境异质性和波动，并能管理多个种群来源。基于合并的方法可生成主要用于群体遗传学研究的遗传标记（DNA 序列、SNP、STR 或 RFLP）。在基于祖先重组图的重组模型下，可以生成各种独立的、完全或部分连锁的遗传标记的组合。也可以模拟两个种群（或物种）之间的竞争，用户可以定义两个种群之间的混合程度。SPLATCHE2 可用于生成复杂的种群动态下的预期遗传多样性，从而可以用来检验零假设。对于模型参数估计，SPLATCHE2 可以很容易地集成到近似贝叶斯计算（ABC）框架中。
SPLATCHE2 是一个用 C++编写的程序，可在 Windows 和 Linux 平台上编译。它可在 www.splatche.com 上免费获得，同时提供相关文档和示例数据。
