Department of Biological Sciences, Macquarie University, Sydney, Australia.
Department of Organismic and Evolutionary Biology, Harvard University, Cambridge, MA.
Mol Biol Evol. 2017 Apr 1;34(4):1016-1020. doi: 10.1093/molbev/msw279.
Bayesian inference using Markov chain Monte Carlo (MCMC) has become one of the primary methods used to infer phylogenies from sequence data. Assessing convergence is a crucial component of these analyses, as it establishes the reliability of the posterior distribution estimates of the tree topology and model parameters sampled from the MCMC. Numerous tests and visualizations have been developed for this purpose, but many of the most popular methods are implemented in ways that make them inconvenient to use for large data sets. RWTY is an R package that implements established and new methods for diagnosing phylogenetic MCMC convergence in a single convenient interface.
贝叶斯推断使用马尔可夫链蒙特卡罗（MCMC）已经成为从序列数据推断系统发育的主要方法之一。评估收敛性是这些分析的一个关键组成部分，因为它确定了从 MCMC 采样的树拓扑和模型参数的后验分布估计的可靠性。为此已经开发了许多测试和可视化方法，但许多最流行的方法的实现方式使得它们对于大数据集的使用不太方便。RWTY 是一个 R 包，它在一个方便的界面中实现了用于诊断系统发育 MCMC 收敛性的既定和新方法。
