MEGA-GPT: Artificial Intelligence Guidance and Building Analytical Protocols Using MEGA Software.

Over the past three decades, the Molecular Evolutionary Genetics Analysis (MEGA) software has evolved into a powerful tool with an ever-expanding suite of functionalities. Yet, despite its user-friendly design and widespread adoption by researchers and students, the software's extensive feature set can overwhelm both new and experienced users who are unfamiliar with its latest capabilities. To address this challenge, we developed MEGA-GPT, an AI-driven resource that leverages ChatGPT augmented with retrieval techniques to guide users through MEGA's analytical workflows via natural language queries. By integrating MEGA's help documentation, version-specific articles, and other key publications, MEGA-GPT enhances ChatGPT's standard responses to deliver step-by-step protocols, clarify analytical settings, and recommend optimal workflows. Our evaluations indicate that MEGA-GPT offers significantly improved guidance while minimizing the hallucinations and inaccuracies observed in standard ChatGPT outputs. We propose that such customized, retrieval-augmented query interfaces can substantially enhance the usability of complex scientific computing packages. MEGA-GPT is freely available to all users with a ChatGPT account by accessing the URL https://tinyurl.com/gpt-mega, which is also integrated into MEGA's graphical user interface.