Moore Ryan M, Harrison Amelia O, McAllister Sean M, Polson Shawn W, Wommack K Eric
Center for Bioinformatics and Computational Biology, University of Delaware, Newark, DE, United States of America.
School of Marine Science and Policy, University of Delaware, Newark, DE, United States of America.
PeerJ. 2020 Feb 26;8:e8584. doi: 10.7717/peerj.8584. eCollection 2020.
Phylogenetic trees are an important analytical tool for evaluating community diversity and evolutionary history. In the case of microorganisms, the decreasing cost of sequencing has enabled researchers to generate ever-larger sequence datasets, which in turn have begun to fill gaps in the evolutionary history of microbial groups. However, phylogenetic analyses of these types of datasets create complex trees that can be challenging to interpret. Scientific inferences made by visual inspection of phylogenetic trees can be simplified and enhanced by customizing various parts of the tree. Yet, manual customization is time-consuming and error prone, and programs designed to assist in batch tree customization often require programming experience or complicated file formats for annotation. Iroki, a user-friendly web interface for tree visualization, addresses these issues by providing automatic customization of large trees based on metadata contained in tab-separated text files. Iroki's utility for exploring biological and ecological trends in sequencing data was demonstrated through a variety of microbial ecology applications in which trees with hundreds to thousands of leaf nodes were customized according to extensive collections of metadata. The Iroki web application and documentation are available at https://www.iroki.net or through the VIROME portal http://virome.dbi.udel.edu. Iroki's source code is released under the MIT license and is available at https://github.com/mooreryan/iroki.
系统发育树是评估群落多样性和进化历史的重要分析工具。对于微生物而言，测序成本的降低使研究人员能够生成规模不断扩大的序列数据集，这些数据集进而开始填补微生物类群进化历史中的空白。然而，对这类数据集进行系统发育分析会产生复杂的树，难以解读。通过对树的各个部分进行定制，可以简化并增强通过直观检查系统发育树得出的科学推断。然而，手动定制既耗时又容易出错，而旨在协助批量树定制的程序通常需要编程经验或复杂的文件格式来进行注释。Iroki是一个用户友好的树可视化网络界面，通过基于制表符分隔文本文件中包含的元数据对大树进行自动定制，解决了这些问题。通过各种微生物生态学应用展示了Iroki在探索测序数据中的生物学和生态学趋势方面的效用，在这些应用中，根据大量元数据集合对具有数百到数千个叶节点的树进行了定制。Iroki网络应用程序和文档可在https://www.iroki.net获取，或通过VIROME门户http://virome.dbi.udel.edu获取。Iroki的源代码根据麻省理工学院许可发布，可在https://github.com/mooreryan/iroki获取。
