IslandViewer 4 is an updated version of the webserver IslandViewer, designed to enhance the prediction and visualization of genomic islands (GIs) in bacterial and archaeal genomes. GIs are regions of probable horizontal origin that often encode factors enhancing microbial adaptability and competitiveness, including virulence factors and antimicrobial resistance genes. The new version includes several key improvements: 1. **User Management and Batch Analysis**: A user management web interface and an HTTP API have been added to facilitate the submission of large numbers of genomes and retrieval of results, with secured authentication. 2. **Improved GI Predictions**: Integrated GI predictions from multiple methods, including the precise Islander method for pre-computed genomes and an updated IslandPath-DIMOB for both pre-computed and custom genome analysis, have been improved and expanded. 3. **Pre-computed Predictions**: Pre-computed predictions for 6193 complete bacterial and archaeal strains are now available, including virulence factors and antimicrobial resistance genes. 4. **Enhanced Visualization**: The interactive visualization interface has been streamlined to produce publication-grade figures, with improved loading times and a more user-friendly layout. 5. **Backend Upgrades**: The database backend has been updated to MariaDB with the Percona XtraDB storage engine, improving scalability and performance. 6. **Faster Genomic Distance Computation**: MASH, a tool for efficient genome similarity measurement, has been integrated to reduce the time required for pairwise genomic distance calculations from hours to minutes. These enhancements make IslandViewer 4 a more comprehensive and flexible tool for the analysis of GIs, facilitating research in microbial evolution and pathogen outbreak analysis.IslandViewer 4 is an updated version of the webserver IslandViewer, designed to enhance the prediction and visualization of genomic islands (GIs) in bacterial and archaeal genomes. GIs are regions of probable horizontal origin that often encode factors enhancing microbial adaptability and competitiveness, including virulence factors and antimicrobial resistance genes. The new version includes several key improvements: 1. **User Management and Batch Analysis**: A user management web interface and an HTTP API have been added to facilitate the submission of large numbers of genomes and retrieval of results, with secured authentication. 2. **Improved GI Predictions**: Integrated GI predictions from multiple methods, including the precise Islander method for pre-computed genomes and an updated IslandPath-DIMOB for both pre-computed and custom genome analysis, have been improved and expanded. 3. **Pre-computed Predictions**: Pre-computed predictions for 6193 complete bacterial and archaeal strains are now available, including virulence factors and antimicrobial resistance genes. 4. **Enhanced Visualization**: The interactive visualization interface has been streamlined to produce publication-grade figures, with improved loading times and a more user-friendly layout. 5. **Backend Upgrades**: The database backend has been updated to MariaDB with the Percona XtraDB storage engine, improving scalability and performance. 6. **Faster Genomic Distance Computation**: MASH, a tool for efficient genome similarity measurement, has been integrated to reduce the time required for pairwise genomic distance calculations from hours to minutes. These enhancements make IslandViewer 4 a more comprehensive and flexible tool for the analysis of GIs, facilitating research in microbial evolution and pathogen outbreak analysis.