HyPhy 2.5-A 可定制的基于系统发生树的进化假说检验平台。
HyPhy 2.5-A Customizable Platform for Evolutionary Hypothesis Testing Using Phylogenies.
机构信息
Institute for Genomics and Evolutionary Medicine, Temple University, Philadelphia, PA.
Pathology and Laboratory Medicine, Western University, London, ON, Canada.
出版信息
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。
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