Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
Pathology and Laboratory Medicine, Western University, London, ON, Canada.
Mol Biol Evol. 2020 Jan 1;37(1):295-299. doi: 10.1093/molbev/msz197.
HYpothesis testing using PHYlogenies (HyPhy) is a scriptable, open-source package for fitting a broad range of evolutionary models to multiple sequence alignments, and for conducting subsequent parameter estimation and hypothesis testing, primarily in the maximum likelihood statistical framework. It has become a popular choice for characterizing various aspects of the evolutionary process: natural selection, evolutionary rates, recombination, and coevolution. The 2.5 release (available from www.hyphy.org) includes a completely re-engineered computational core and analysis library that introduces new classes of evolutionary models and statistical tests, delivers substantial performance and stability enhancements, improves usability, streamlines end-to-end analysis workflows, makes it easier to develop custom analyses, and is mostly backward compatible with previous HyPhy releases.
使用 PHYlogenies (HyPhy) 进行假设检验是一个可脚本化的、开源的包,用于将广泛的进化模型拟合到多个序列比对中,并进行随后的参数估计和假设检验,主要是在最大似然统计框架内。它已成为描述进化过程各个方面的流行选择:自然选择、进化率、重组和共进化。2.5 版本(可从 www.hyphy.org 获得)包括一个完全重新设计的计算核心和分析库,引入了新类别的进化模型和统计检验,提供了实质性的性能和稳定性增强,提高了可用性,简化了端到端分析工作流程,使开发自定义分析变得更加容易,并与以前的 HyPhy 版本基本向后兼容。