Prokaryotes are asexual, but these organisms frequently engage in homologous recombination, a process that differs from meiotic recombination in sexual organisms. Most tools developed to simulate genome evolution either assume sexual reproduction or the complete absence of DNA flux in the population. As a result, very few simulators are adapted to model prokaryotic genome evolution while accounting for recombination. Moreover, many simulators are based on the coalescent, which assumes a neutral model of genomic evolution, and those are best suited for organisms evolving under weak selective pressures, such as animals and plants. In contrast, prokaryotes are thought to be evolving under much stronger selective pressures, suggesting that forward-in-time simulators are better suited for these organisms. Here, I present CoreSimul, a forward-in-time simulator of core genome evolution for prokaryotes modeling homologous recombination. Simulations are guided by a phylogenetic tree and incorporate different substitution models, including models of codon selection. CoreSimul is a flexible forward-in-time simulator that constitutes a significant addition to the limited list of available simulators applicable to prokaryote genome evolution.

中文翻译：

---

CoreSimul：用于模拟同源重组的原核生物的基因组进化的实时仿真器。

原核生物是无性的，但是这些生物经常参与同源重组，这一过程不同于性生物中的减数分裂重组。为模拟基因组进化而开发的大多数工具都假定有性繁殖或种群中完全没有DNA流通。结果，很少有模拟器能够模拟原核基因组进化，同时考虑到重组。而且，许多模拟器都基于合并模型，该模型假定了基因组进化的中性模型，并且最适合于在弱选择压力下进化的生物，例如动植物。相反，原核生物被认为是在更大的选择性压力下进化的，这表明及时的模拟器更适合于这些生物。在这里，我介绍CoreSimul，核心基因组进化的实时模拟器，用于对原核生物进行同源重组建模。模拟以系统发育树为指导，并结合了不同的替代模型，包括密码子选择模型。CoreSimul是一种灵活的实时转发模拟器，在适用于原核生物基因组进化的可用模拟器的有限列表中构成了重要的补充。