Testing Multispecies Coalescent Simulators Using Summary Statistics
Testing Multispecies Coalescent Simulators Using Summary Statistics
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DOI：
10.1109/tcbb.2022.3177956
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发表时间：
2023-03-01
影响因子：
4.5
通讯作者：
Rhodes，John A.
中科院分区：
文献类型：
--
作者：
Allman，Elizabeth S.;Banos，Hector;Rhodes，John A.
由于基因组规模的数据集激发了物种树推理的研究，多物种合并（MSC）过程的模拟器已成为测试和评估新推理方法的关键。然而，模拟器本身必须进行测试，以确保它们提供有效的样本。这项工作开发的方法来检查是否收集的基因树是在雅阁符合MSC模型上一个给定的物种树。当应用到著名的模拟器，我们发现，有几个给有缺陷的样本。所提出的测试能够验证基因树样本的拓扑和度量性质，并在一个免费提供的R软件包MSCsimtester中实现，以便开发人员和用户可以很容易地应用它们。
As genomic-scale datasets motivate research on species tree inference, simulators of the multispecies coalescent (MSC) process have become essential for the testing and evaluation of new inference methods. However, the simulators themselves must be tested to ensure that they give valid samples. This work develops methods for checking whether a collection of gene trees is in accord with the MSC model on a given species tree. When applied to well-known simulators, we find that several give flawed samples. The tests presented are capable of validating both topological and metric properties of gene tree samples, and are implemented in a freely available R packageMSCsimtesterso that developers and users may easily apply them.