MCScanX is a toolkit for detecting and analyzing gene synteny and collinearity. It extends the original MCScan algorithm by incorporating 14 utility programs for visualization and downstream analysis. MCScanX can effectively analyze chromosome structural changes and reveal the history of gene family expansions. It provides an integrated view of various gene duplication modes, aiding in the construction of gene families, inference of duplication modes, and characterization of collinear genes. The toolkit is freely available at http://chibba.pgml.uga.edu/mcscan2/. MCScanX uses whole-genome BLASTP results to identify collinear blocks and perform multi-alignments using collinear genes as anchors. It is customizable for different genome sizes and intergenic distances. MCScanX simplifies the usage of MCScan and provides various visualization and analysis tools. It can detect collinear blocks, classify duplicate gene origins, and analyze gene family evolution. MCScanX also allows for the detection of collinear orthologs and collinear tandem arrays, and can perform statistical analyses of duplication depths and collinear orthologs. MCScanX is compared with other synteny and collinearity detection tools and is found to be more comprehensive, offering five functions: detection of synteny and collinearity, visualization, evolutionary analysis, gene family analysis, and statistical analysis. It is more efficient than other tools in detecting collinear gene pairs and has higher power and precision in identifying collinear gene pairs. MCScanX is applicable to a wide range of organisms beyond angiosperms. The toolkit is useful for analyzing chromosome structural changes, annotating new genomes, and revealing the history of gene family expansions. It is freely available and has been applied to various research areas, including genome duplication and evolution, annotation of newly sequenced genomes, and the evolution of gene families. MCScanX provides a powerful tool for the analysis of gene synteny and collinearity, enabling the conversion of synteny and collinearity information into evolutionary insights.MCScanX is a toolkit for detecting and analyzing gene synteny and collinearity. It extends the original MCScan algorithm by incorporating 14 utility programs for visualization and downstream analysis. MCScanX can effectively analyze chromosome structural changes and reveal the history of gene family expansions. It provides an integrated view of various gene duplication modes, aiding in the construction of gene families, inference of duplication modes, and characterization of collinear genes. The toolkit is freely available at http://chibba.pgml.uga.edu/mcscan2/. MCScanX uses whole-genome BLASTP results to identify collinear blocks and perform multi-alignments using collinear genes as anchors. It is customizable for different genome sizes and intergenic distances. MCScanX simplifies the usage of MCScan and provides various visualization and analysis tools. It can detect collinear blocks, classify duplicate gene origins, and analyze gene family evolution. MCScanX also allows for the detection of collinear orthologs and collinear tandem arrays, and can perform statistical analyses of duplication depths and collinear orthologs. MCScanX is compared with other synteny and collinearity detection tools and is found to be more comprehensive, offering five functions: detection of synteny and collinearity, visualization, evolutionary analysis, gene family analysis, and statistical analysis. It is more efficient than other tools in detecting collinear gene pairs and has higher power and precision in identifying collinear gene pairs. MCScanX is applicable to a wide range of organisms beyond angiosperms. The toolkit is useful for analyzing chromosome structural changes, annotating new genomes, and revealing the history of gene family expansions. It is freely available and has been applied to various research areas, including genome duplication and evolution, annotation of newly sequenced genomes, and the evolution of gene families. MCScanX provides a powerful tool for the analysis of gene synteny and collinearity, enabling the conversion of synteny and collinearity information into evolutionary insights.