MCScanX is a toolkit designed for the detection and evolutionary analysis of gene synteny and collinearity. It extends the original MCScan algorithm by incorporating 14 utility programs for visualization and downstream analyses. The toolkit can be used to analyze chromosome structural changes, reveal the history of gene family expansions, and provide insights into genome evolution. MCScanX is particularly useful for studying the evolutionary history of genomes, such as angiosperms, which have undergone significant genome restructuring, and vertebrates, which have experienced slower evolutionary changes. The software package is freely available and can be used to generate both pairwise and multiple alignments of collinear blocks, classify duplicate genes, and perform various types of plots and analyses. Compared to other synteny and collinearity detection tools, MCScanX offers a more integrated approach, enabling rapid and convenient conversion of synteny and collinearity information into evolutionary insights.MCScanX is a toolkit designed for the detection and evolutionary analysis of gene synteny and collinearity. It extends the original MCScan algorithm by incorporating 14 utility programs for visualization and downstream analyses. The toolkit can be used to analyze chromosome structural changes, reveal the history of gene family expansions, and provide insights into genome evolution. MCScanX is particularly useful for studying the evolutionary history of genomes, such as angiosperms, which have undergone significant genome restructuring, and vertebrates, which have experienced slower evolutionary changes. The software package is freely available and can be used to generate both pairwise and multiple alignments of collinear blocks, classify duplicate genes, and perform various types of plots and analyses. Compared to other synteny and collinearity detection tools, MCScanX offers a more integrated approach, enabling rapid and convenient conversion of synteny and collinearity information into evolutionary insights.