TYGS is an automated high-throughput platform for genome-based microbial taxonomy. It provides a user-friendly web server with a large database of genomic, taxonomic, and nomenclatural information. TYGS infers genome-scale phylogenies and estimates species and subspecies boundaries using closest type genome sequences. It also offers access to nomenclature, synonymy, and taxonomic literature. TYGS is particularly useful for classifying new genera, species, or subspecies. It integrates data validation and methods in a single platform, enabling high-throughput analysis without manual interaction. TYGS outperforms traditional methods like DDH and 16S rRNA gene analysis, offering more accurate and standardized results. It is especially helpful for taxonomists and microbiologists in the field of genome-based taxonomy. TYGS has been tested on clinically important data sets, such as Mycobacterium and Salmonella, revealing new insights into microbial classification. For example, it showed that some previously proposed subspecies of Salmonella enterica should be elevated to species status. TYGS also provides a comprehensive database of type strain genomes, enabling the identification of closest relatives and phylogenetic analysis. It supports both genome-based and 16S rRNA gene-based phylogenetic approaches. TYGS is freely available and publicly accessible, making it a valuable tool for microbial systematics. The platform uses advanced computational methods, including GBDP, to infer phylogenetic trees and calculate branch support. It also includes features for detecting and analyzing type strains, ensuring accurate taxonomic classification. TYGS is an integrated approach that facilitates the classification of microbes, offering a unique combination of tools for microbiologists, taxonomists, and health professionals.TYGS is an automated high-throughput platform for genome-based microbial taxonomy. It provides a user-friendly web server with a large database of genomic, taxonomic, and nomenclatural information. TYGS infers genome-scale phylogenies and estimates species and subspecies boundaries using closest type genome sequences. It also offers access to nomenclature, synonymy, and taxonomic literature. TYGS is particularly useful for classifying new genera, species, or subspecies. It integrates data validation and methods in a single platform, enabling high-throughput analysis without manual interaction. TYGS outperforms traditional methods like DDH and 16S rRNA gene analysis, offering more accurate and standardized results. It is especially helpful for taxonomists and microbiologists in the field of genome-based taxonomy. TYGS has been tested on clinically important data sets, such as Mycobacterium and Salmonella, revealing new insights into microbial classification. For example, it showed that some previously proposed subspecies of Salmonella enterica should be elevated to species status. TYGS also provides a comprehensive database of type strain genomes, enabling the identification of closest relatives and phylogenetic analysis. It supports both genome-based and 16S rRNA gene-based phylogenetic approaches. TYGS is freely available and publicly accessible, making it a valuable tool for microbial systematics. The platform uses advanced computational methods, including GBDP, to infer phylogenetic trees and calculate branch support. It also includes features for detecting and analyzing type strains, ensuring accurate taxonomic classification. TYGS is an integrated approach that facilitates the classification of microbes, offering a unique combination of tools for microbiologists, taxonomists, and health professionals.