King Kelly M, Van Doorslaer Koenraad
School of Animal and Comparative Biomedical Sciences, University of Arizona, Tucson, Arizona.
Department of Immunobiology, Cancer Biology Graduate Interdisciplinary Program, Genetics Graduate Interdisciplinary Program, BIO5 Institute, and the University of Arizona Cancer Center, University of Arizona, Tucson, Arizona.
Curr Protoc Microbiol. 2018 Nov;51(1):e63. doi: 10.1002/cpmc.63. Epub 2018 Sep 28.
Phylogenetic analyses allow for inferring a hypothesis about the evolutionary history of a set of homologous molecular sequences. This hypothesis can be used as the basis for further molecular and computational studies. In this unit, we offer one specific method to construct a Maximum Likelihood phylogenetic tree. We outline how to identify homologous sequences and construct a multiple sequence alignment. Following alignment, sequences are screened for potentially confounding factors such as recombination and genetic saturation. Finally, a Maximum Likelihood phylogenetic tree can be constructed implementing a rigorously tested model of evolution. The workflow outlined in this unit provides sufficient background for inferring a robust phylogenetic tree starting from a particular gene of interest. © 2018 by John Wiley & Sons, Inc.
系统发育分析有助于推断一组同源分子序列的进化历史假说。该假说可作为进一步分子和计算研究的基础。在本单元中，我们提供一种构建最大似然系统发育树的具体方法。我们概述了如何识别同源序列并构建多序列比对。比对之后，筛选序列中潜在的混杂因素，如重组和遗传饱和。最后，使用经过严格测试的进化模型构建最大似然系统发育树。本单元概述的工作流程为从特定感兴趣基因推断稳健的系统发育树提供了足够的背景知识。© 2018 约翰威立父子出版公司。
