This course covers the main research areas of comparative genomics in six modules. The first module introduces integrative visualization of genomic features, including gene density, TE content, SNP/InDel density, DNA methylation, histone modifications, and structural variants combined with synteny information. The second module focuses on gene family clustering, explaining ortholog/paralog concepts and demonstrating OrthoFinder workflow, result interpretation, and Venn diagram generation. The third module systematically addresses phylogenetic tree construction, covering rooted/unrooted trees, bootstrap evaluation, gene tree vs. species tree distinctions, and a detailed pipeline for species‑tree building using single‑copy genes: multiple alignment, codon alignment conversion, alignment refinement, model selection, IQ‑TREE inference, and divergence time estimation. The fourth module covers gene family expansion and contraction analysis using CAFE with a dated tree to infer ancestral family sizes and identify significantly expanded/contracted families. The fifth module presents positive selection analysis, introducing the Ka/Ks ratio principle and the branch‑site model in PAML to detect positively selected genes and critical amino acid sites. The sixth module addresses synteny and whole‑genome duplication (WGD) identification, explaining gene‑level and genome‑level synteny methods (MCScanX and MUMMER), and the use of synteny dot‑plots, Ks distributions, and 4DTv distributions to detect ancient polyploidy events. The course integrates case studies from high‑impact publications, bridging theory and practice for researchers in comparative genomics and evolutionary biology.