It has become increasingly challenging for researchers to analyze the exponentially expanding multi-omic data. In this project, we have developed a multi-functional software named evolutionary Genotype-Phenotype Systems (eGPS) that enables users to perform comprehensive multi-omic and evolutionary analyses. The eGPS has a user-friendly graphic interface, and is highly interactive. 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 not only develops the new functions/tools/methods but also bridges the gap between multi-omic and evolutionary analyses.