Department of Biological Sciences, Tokyo Metropolitan University, Tokyo, Japan.
Research Center for Genomics and Bioinformatics, Tokyo Metropolitan University, Tokyo, Japan.
Mol Biol Evol. 2021 Jun 25;38(7):3022-3027. doi: 10.1093/molbev/msab120.
The Molecular Evolutionary Genetics Analysis (MEGA) software has matured to contain a large collection of methods and tools of computational molecular evolution. Here, we describe new additions that make MEGA a more comprehensive tool for building timetrees of species, pathogens, and gene families using rapid relaxed-clock methods. Methods for estimating divergence times and confidence intervals are implemented to use probability densities for calibration constraints for node-dating and sequence sampling dates for tip-dating analyses. They are supported by new options for tagging sequences with spatiotemporal sampling information, an expanded interactive Node Calibrations Editor, and an extended Tree Explorer to display timetrees. Also added is a Bayesian method for estimating neutral evolutionary probabilities of alleles in a species using multispecies sequence alignments and a machine learning method to test for the autocorrelation of evolutionary rates in phylogenies. The computer memory requirements for the maximum likelihood analysis are reduced significantly through reprogramming, and the graphical user interface has been made more responsive and interactive for very big data sets. These enhancements will improve the user experience, quality of results, and the pace of biological discovery. Natively compiled graphical user interface and command-line versions of MEGA11 are available for Microsoft Windows, Linux, and macOS from www.megasoftware.net.
《分子进化遗传学分析（MEGA）软件已经发展成熟，包含了大量计算分子进化的方法和工具。在这里，我们描述了新的添加功能，使 MEGA 成为更全面的工具，可用于使用快速松弛时钟方法构建物种、病原体和基因家族的时间树。用于估计分歧时间和置信区间的方法实现了使用校准约束的概率密度进行节点定年和序列采样日期进行尖端定年分析。这些方法得到了新选项的支持，这些选项可用于标记具有时空采样信息的序列，扩展的交互式节点校准编辑器，以及用于显示时间树的扩展树浏览器。还添加了一种使用多物种序列比对估计物种中等位基因中性进化概率的贝叶斯方法，以及一种用于测试系统发育中进化率自相关的机器学习方法。通过重新编程，最大似然分析的计算机内存要求大大降低，图形用户界面变得更加响应和交互，适用于非常大数据集。这些增强功能将提高用户体验、结果质量和生物学发现的速度。MEGA11 的本机编译图形用户界面和命令行版本可从 www.megasoftware.net 获得，适用于 Microsoft Windows、Linux 和 macOS。
