Building Phylogenetic Trees from Molecular Data with MEGA
Building Phylogenetic Trees from Molecular Data with MEGA
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DOI：
10.1093/molbev/mst012
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发表时间：
2013-05-01
影响因子：
10.7
通讯作者：
Hall, Barry G.
中科院分区：
文献类型：
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作者：
Hall, Barry G.
系统发育分析有时被认为是一个令人生畏的复杂过程，需要专业知识和多年的经验。事实上，这是一个相当简单的过程，可以快速学习和有效应用。该方案描述了从新手的分子数据生成系统发育树所需的几个步骤。在这里所示的示例中，程序MEGA用于实现所有这些步骤，从而消除了学习几个程序的需要，并且从一个步骤到另一个步骤处理多种文件格式（Tamura K，Peterson D，Peterson N，Stecher G，Nei M，Kumar S. 2011. MEGA 5：使用最大似然、进化距离和最大简约方法进行分子进化遗传学分析。分子生物学评价28：2731-2739）。第一步，识别一组同源序列并下载这些序列，是由MEGA自己的浏览器在Google Chrome工具包上实现的。对于第二步，这些序列的比对，MEGA提供了两种不同的算法：ClustalW和MUSCLE。对于第三步，从比对序列构建系统发育树，MEGA提供了许多不同的方法。在这里，我们说明了最大似然方法，从MEGA的模型功能开始，它允许选择最合适的替代模型。最后，MEGA为最后一步提供了一个强大而灵活的界面，实际上是绘制用于发布的树。在这里，一步一步的协议，提出了足够的细节，让新手开始与感兴趣的序列，并建立一个出版质量的树，说明了该序列的同源物的一组适当的演变。MEGA可在PC和Mac上使用，网址为www.megasoftware.net。
Phylogenetic analysis is sometimes regarded as being an intimidating, complex process that requires expertise and years of experience. In fact, it is a fairly straightforward process that can be learned quickly and applied effectively. This Protocol describes the several steps required to produce a phylogenetic tree from molecular data for novices. In the example illustrated here, the program MEGA is used to implement all those steps, thereby eliminating the need to learn several programs, and to deal with multiple file formats from one step to another (Tamura K, Peterson D, Peterson N, Stecher G, Nei M, Kumar S. 2011. MEGA5: molecular evolutionary genetics analysis using maximum likelihood, evolutionary distance, and maximum parsimony methods. Mol Biol Evol. 28:2731-2739). The first step, identification of a set of homologous sequences and downloading those sequences, is implemented by MEGA's own browser built on top of the Google Chrome toolkit. For the second step, alignment of those sequences, MEGA offers two different algorithms: ClustalW and MUSCLE. For the third step, construction of a phylogenetic tree from the aligned sequences, MEGA offers many different methods. Here we illustrate the maximum likelihood method, beginning with MEGA's Models feature, which permits selecting the most suitable substitution model. Finally, MEGA provides a powerful and flexible interface for the final step, actually drawing the tree for publication. Here a step-by-step protocol is presented in sufficient detail to allow a novice to start with a sequence of interest and to build a publication-quality tree illustrating the evolution of an appropriate set of homologs of that sequence. MEGA is available for use on PCs and Macs from www.megasoftware.net.