TYGS (Type (Strain) Genome Server) is an automated, high-throughput web platform for genome-based prokaryote taxonomy. It integrates a large, continuously growing database of genomic, taxonomic, and nomenclatural information, enabling the inference of genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries. TYGS provides comprehensive access to nomenclature, synonymy, and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of *Salmonella enterica*. TYGS is an integrated approach that unlocks novel scientific methods for microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species, or subspecies.TYGS (Type (Strain) Genome Server) is an automated, high-throughput web platform for genome-based prokaryote taxonomy. It integrates a large, continuously growing database of genomic, taxonomic, and nomenclatural information, enabling the inference of genome-scale phylogenies and state-of-the-art estimates for species and subspecies boundaries. TYGS provides comprehensive access to nomenclature, synonymy, and associated taxonomic literature. Clinically important examples demonstrate how TYGS can yield new insights into microbial classification, such as evidence for a species-level separation of previously proposed subspecies of *Salmonella enterica*. TYGS is an integrated approach that unlocks novel scientific methods for microbiologists worldwide and is particularly helpful for the rapidly expanding field of genome-based taxonomic descriptions of new genera, species, or subspecies.