A new era of evolutionary analysis based on a personal computer: the future of multifunctional software such as eGPS.
Dalang Yu, Jianing Yang, Jianwei Zhang, Wanyu Zhang, Haipeng Li · PubMed · 2025
The large-scale data generated by various omics technologies pose significant scientific challenges about how to rapidly and accurately analyze these data. It is essential to develop convenient tools that allow users to efficiently and precisely handle massive biological data. Based on new theories and mathematical models, as well as software engineering, this field is becoming an important research direction in bioinformatics and computational biology. In this review, we briefly review the development history of bioinformatics-related software. We also summarize the recent progress, focus on their application on evolutionary biology, and discuss three major ways of computer running mode and three paradigms of software programming. We also introduce the eGPS, a self-developed multi-functional evolutionary and omics analysis software platform, including the application of eGPS along with Conda and R for data analysis on individual genes, pathways, or genomes. We then propose new ideas for software development, use, and maintenance tailored to different users with varying scientific objectives. It posits that using a personal computer for evolutionary and multi-omics analysis is not only a necessity but also playing an important role.