Eras of bioinformatics technologies from command-line interfaces to artificial intelligence (AI) chatbots

Over the past 75 years, especially the recent quarter century, bioinformatics has undergone a profound transformation, evolving from a specialized field of command-line tools to a cornerstone of modern biomedical and life sciences. We trace this journey through distinct technological eras driven by exponential biological data growth and parallel computational advances. The genomic revolution established foundational sequence analysis tools and was rapidly followed by the next-generation sequencing era, when unprecedented data volumes shifted the bottleneck from generation to analysis. This drove the development of web servers, cloud platforms, and containerized workflows to address scalability, accessibility, and reproducibility challenges. We now stand in the artificial intelligence (AI)-driven era, where deep learning (e.g. AlphaFold series) and large language models reshape structural biology, multi-modal data integration, and how researchers interact with tools through natural language prompting. This review highlights a recurring pattern as each technological era lowers barriers to entry, it simultaneously introduces new questions about transparency, trust, and rigor. By framing the popular rise of AI within this historical context, we provide a critical roadmap for navigating the cultural, ethical, and technical crossroads facing the next generation of bioinformatics.