PHAge Search Tool (PHAST) is a web-based tool designed to rapidly and accurately identify, annotate, and display prophage sequences within bacterial genomes or plasmids. It supports both raw DNA sequence data and partially annotated GenBank formatted data, performing multiple database comparisons and phage 'cornerstone' feature identification to locate and annotate prophage sequences. Compared to other prophage identification tools, PHAST is up to 40 times faster and 15% more sensitive. It can process raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and quality, and distinguish between intact and incomplete prophage. PHAST generates high-quality, interactive graphics for visualizing identified prophage components in both circular and linear genomic views. The tool is available at http://phast.wishartlab.com.PHAge Search Tool (PHAST) is a web-based tool designed to rapidly and accurately identify, annotate, and display prophage sequences within bacterial genomes or plasmids. It supports both raw DNA sequence data and partially annotated GenBank formatted data, performing multiple database comparisons and phage 'cornerstone' feature identification to locate and annotate prophage sequences. Compared to other prophage identification tools, PHAST is up to 40 times faster and 15% more sensitive. It can process raw DNA sequence data and Genbank files, provide richly annotated tables on prophage features and quality, and distinguish between intact and incomplete prophage. PHAST generates high-quality, interactive graphics for visualizing identified prophage components in both circular and linear genomic views. The tool is available at http://phast.wishartlab.com.