WEGO is a web-based tool for visualizing, comparing, and plotting Gene Ontology (GO) annotation results. It is designed to handle the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO is user-friendly, operating system-independent, and allows users to upload annotation files in various formats, including WEGO native, InterProScan raw, text, and XML. It supports the comparison of multiple gene datasets and provides visualization of annotation results. WEGO also includes two associated tools: External to GO Query and GO Archive Query, which help users translate between other categories and GO terms, and query GO IDs across different versions of the GO archive. WEGO is freely available at http://wego.genomics.org.cn and has been widely used in biological research projects, such as the rice genome and silkworm genome studies. It is an essential tool for downstream gene annotation analysis, especially in comparative genomics. The output of WEGO is in SVG format, which is widely supported and can be converted to other graph formats. WEGO aims to be a user-friendly tool for biologists, especially those without computer backgrounds, and is designed to integrate with other GO tools in the future.WEGO is a web-based tool for visualizing, comparing, and plotting Gene Ontology (GO) annotation results. It is designed to handle the directed acyclic graph (DAG) structure of GO to facilitate histogram creation of GO annotation results. WEGO is user-friendly, operating system-independent, and allows users to upload annotation files in various formats, including WEGO native, InterProScan raw, text, and XML. It supports the comparison of multiple gene datasets and provides visualization of annotation results. WEGO also includes two associated tools: External to GO Query and GO Archive Query, which help users translate between other categories and GO terms, and query GO IDs across different versions of the GO archive. WEGO is freely available at http://wego.genomics.org.cn and has been widely used in biological research projects, such as the rice genome and silkworm genome studies. It is an essential tool for downstream gene annotation analysis, especially in comparative genomics. The output of WEGO is in SVG format, which is widely supported and can be converted to other graph formats. WEGO aims to be a user-friendly tool for biologists, especially those without computer backgrounds, and is designed to integrate with other GO tools in the future.