This Phage Atlas was generated with the Hierarchical Viruses (HieVi) pipeline we developed to explore the bacteriophage world diversity using machine learning-based representations. HieVi harnesses the Evolutionary Scale Model 2 (ESM-2) protein Language Model (pLM) to describe entire viral proteomes. We organized bacteriophages in a hierarchical tree that captures multiscale evolutionary relationships in good accordance with established bacteriophage phylogenies. HieVi is the first example of pLM implementation to sort and compare biological entities, opening new perspectives for comparative genomics for biologists in the field.