eGPS 1.0: comprehensive software for multi-omic and evolutionary analyses

作者：Dalang Yu, Lili Dong, Fangqi Yan, Hailong Mu, Bixia Tang, Xiao Yang, Tao Zeng, Qing Zhou, Feng Gao, Zhonghuang Wang, Zi-Qian Hao, Hongen Kang, Yi Zheng, Hongwei Huang, Yuzhang Wei, Wei Pan, Yaochen Xu, Junwei Zhu, Shilei Zhao, Ciran Wang, Pengyu Wang, Long Dai, Mushan Li, Lan Li, Yiwei Wang, Hua Chen, Yixue Li, Yun‐Xin Fu, Zhen Shao, Yīmíng Bào, Fangqing Zhao, Luonan Chen, Guoqing Zhang, Wenming Zhao, Haipeng Li · 发表于：National Science Review · 年份：2019 · DOI：10.1093/nsr/nwz079 · 被引用次数：33 · 研究领域：Bioinformatics and Genomic Networks、Evolution and Genetic Dynamics、Genomics and Phylogenetic Studies

It has become increasingly challenging for researchers to analyze the exponentially expanding amount of multi-omic data. Here, we describe multi-functional software named evolutionary Genotype-Phenotype Systems (eGPS) that enables users to perform comprehensive multi-omic and evolutionary analyses. The eGPS combines the power of cloud computing and the advantage of desktop application, has a user-friendly graphic interface and is highly interactive. Moreover, third-party plug-ins are supported and their developers can take the credit for contributing the plug-ins. This makes it easier for the community to implement new modules and also encourages their sharing. The eGPS not only develops new functions, tools and methods, but also bridges the gap between multi-omic and evolutionary analyses. The eGPS cloud and desktop application are freely available at http://www.egps-software.org/. As a new and comprehensive piece of software, eGPS contains more than 20 popular methods and 20 data visualization tools that cover genomics, population genetics, evolutionary biology, differential gene expression and network data analyses. Users can consult the eGPS website and the user manual for further information. The new major functions implemented by the eGPS are outlined below. Based on a high-performance computer environment, the eGPS cloud integrates resources for computing and data storage (Fig. 1A). The eGPS cloud is focused on facilitating user-friendly application development (includ...