SLiM 2: Flexible, Interactive Forward Genetic Simulations
SLiM 2: Flexible, Interactive Forward Genetic Simulations
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DOI：
10.1093/molbev/msw211
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发表时间：
2017-01-01
影响因子：
10.7
通讯作者：
Messer, Philipp W.
中科院分区：
文献类型：
--
作者：
Haller, Benjamin C.;Messer, Philipp W.
现代群体基因组数据集对于揭示自然群体中的进化过程有着巨大的希望，但实现这一目标的一个关键先决条件是能够模拟现实的进化场景并预测其在基因组数据中的预期模式。为此，我们推出了 SLiM 2：一种进化模拟框架，它将用于正向种群遗传模拟的强大、快速引擎与对各种复杂进化场景进行建模的能力相结合。 SLiM 通过脚本化实现了这种灵活性，它通过一种名为 Eidos 的简单的类似 R 的脚本语言来控制模拟进化场景的大多数方面。我们提供了一个 SLiM 仿真示例来说明该方法的强大功能。 SLiM 2 还包括用于仿真构建、交互式运行时控制和仿真输出动态可视化的图形用户界面，通过快速原型设计和可视化调试，促进轻松快速的模型开发。最后，我们对 SLiM 和其他两个流行的正向遗传模拟软件包进行了性能比较。
Modern population genomic datasets hold immense promise for revealing the evolutionary processes operating in natural populations, but a crucial prerequisite for this goal is the ability to model realistic evolutionary scenarios and predict their expected patterns in genomic data. To that end, we present SLiM 2: an evolutionary simulation framework that combines a powerful, fast engine for forward population genetic simulations with the capability of modeling a wide variety of complex evolutionary scenarios. SLiM achieves this flexibility through scriptability, which provides control over most aspects of the simulated evolutionary scenarios with a simple R-like scripting language called Eidos. An example SLiM simulation is presented to illustrate the power of this approach. SLiM 2 also includes a graphical user interface for simulation construction, interactive runtime control, and dynamic visualization of simulation output, facilitating easy and fastmodel development with quick prototyping and visual debugging. We conclude with a performance comparison between SLiM and two other popular forward genetic simulation packages.