The complete workflow of gene family analysis is divided into four major modules. The first module focuses on member identification, guiding users to obtain sequences from databases such as NCBI and Phytozome, integrating BLAST homology searches with HMM-based conserved domain detection, and applying strict filtering using databases like Pfam and CDD to ensure accurate and non-redundant results. The second module systematically covers gene family characterization, including physicochemical property calculations, subcellular localization prediction, chromosomal location visualization, motif and conserved domain identification, gene structure display, and promoter cis-element analysis, along with demonstrations of multi-dimensional data integration and visualization techniques. The third module delves into evolutionary analysis methods, introducing fundamental phylogenetic tree terminology, bootstrap reliability assessment, principles of distance-based and maximum likelihood tree construction, and practical applications of software such as MEGA and IQ-TREE, providing guidance for subfamily classification and functional inference. The fourth module emphasizes collinearity analysis and selection pressure estimation, utilizing McScanX to identify syntenic blocks and calculating Ka/Ks ratios to evaluate selective pressures acting on duplicated genes, thereby offering molecular evolutionary insights into gene family expansion and functional diversification. This course balances theoretical foundations with practical tools, serving as a valuable resource for researchers in comparative and functional genomics.