Biopython

Biopython remains the indispensable backbone of computational biology in 2026, serving as the primary bridge between raw biological data and high-performance AI/ML pipelines. As a distributed collaborative project, it provides a comprehensive suite of Python modules designed to handle the complexity of biological data formats including FASTA, GenBank, PDB, and more. Its architecture is built for interoperability, allowing seamless integration with the modern scientific Python stack (NumPy, SciPy, Pandas, and Matplotlib). In the 2026 landscape, Biopython has become a critical pre-processing layer for transformer-based protein language models (PLMs) and genomic LLMs, providing the necessary parsers and structural filters to clean datasets for training. It offers specialized sub-packages for sequence alignment, population genetics, phylogenetics, and structural bioinformatics. Its Bio.PDB module is a standard for researchers working on protein-ligand docking and molecular dynamics. Biopython is released under the Biopython License Agreement, making it freely available for both academic and commercial applications without the restrictive clauses of some GPL-based alternatives.