Department of Bioinformatics and Genomics, University of North Carolina at Charlotte, Charlotte, NC 28223.
Microbiol Spectr. 2019 Jul;7(4). doi: 10.1128/microbiolspec.AME-0006-2018.
In this review, which is a part of the Curated Collection: Advances in Molecular Epidemiology of Infectious Diseases, I present an overview of the principles used to classify organisms in the field of phylogenetics, highlight the methods used to infer the interrelationships of organisms, and summarize how these concepts are applied to molecular epidemiologic analyses. I present steps in analyses that come downstream of the assembly of a set of genomes or genes and the production of a multiple-sequence alignment or other matrices of putative orthologs for comparison. I focus on the history of the problem of phylogenetic reconstruction and debates within the field about the most appropriate methods. I illustrate methods that bridge the gap between molecular epidemiology and traditional epidemiology, including phylogenetic character evolution and geographic visualization. Finally, I provide practical advice on how to conduct an example analysis in the appendix. *This article is part of a curated collection.
在这篇评论中，我概述了系统发生学领域中用于分类生物体的原则，强调了用于推断生物体相互关系的方法，并总结了如何将这些概念应用于分子流行病学分析。我介绍了在组装一组基因组或基因并生成多序列比对或其他假定直系同源矩阵进行比较之后的分析步骤。我专注于系统发育重建问题的历史以及该领域内关于最合适方法的争论。我举例说明了弥合分子流行病学和传统流行病学之间差距的方法，包括系统发育特征进化和地理可视化。最后，我在附录中提供了关于如何进行示例分析的实用建议。*本文是精选集的一部分。
