We have jointly developed a multi-functional software named evolutionary Genotype-Phenotype System (eGPS) that enables users to perform comprehensive multi-omic and evolutionary analyses. It combines the power of cloud computing and the advantage of desktop application, and is highly interactive with a user-friendly graphic interface. Moreover, third-party plugins are supported and the developers can take the credits for contributing the plugins. This makes it easier for the community to implement new modules and also encourages their sharing. The eGPS Cloud and Desktop application are freely available at http://www.egps-software.org/. This research was published online in the article entitled “eGPS 1.0: Comprehensive software for multi-omic and evolutionary analyses” in National Science Review on June 18, 2019.