WEGO (Web Gene Ontology Annotation Plot) is a web-based tool designed to visualize, compare, and plot Gene Ontology (GO) annotation results. Unlike other commercial software, WEGO is tailored to handle the directed acyclic graph structure of GO, facilitating the creation of histograms for GO annotation data. It has been widely used in significant biological research projects, such as the rice and silkworm genome projects, and has become a standard tool for downstream gene annotation analysis, particularly in comparative genomics tasks. WEGO is user-friendly, operating system independent, and supports multiple input formats. It provides a hierarchical GO tree for selecting GO terms and displays gene numbers, percentages, and $P$-values from Pearson Chi-square tests. The tool also includes two associated tools: External to GO Query for translating between GO and other catalogs, and GO Archive Query for selecting the correct version of GO data. WEGO is freely available at http://wego.genomics.org.cn, with mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn.WEGO (Web Gene Ontology Annotation Plot) is a web-based tool designed to visualize, compare, and plot Gene Ontology (GO) annotation results. Unlike other commercial software, WEGO is tailored to handle the directed acyclic graph structure of GO, facilitating the creation of histograms for GO annotation data. It has been widely used in significant biological research projects, such as the rice and silkworm genome projects, and has become a standard tool for downstream gene annotation analysis, particularly in comparative genomics tasks. WEGO is user-friendly, operating system independent, and supports multiple input formats. It provides a hierarchical GO tree for selecting GO terms and displays gene numbers, percentages, and $P$-values from Pearson Chi-square tests. The tool also includes two associated tools: External to GO Query for translating between GO and other catalogs, and GO Archive Query for selecting the correct version of GO data. WEGO is freely available at http://wego.genomics.org.cn, with mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn.