Transposable elements (TEs) are dynamic genomic sequences that significantly influence genome architecture and function. Their ability to move and replicate within the genome positions makes them key drivers of genetic diversity and evolution. Understanding the role of TEs in shaping phenotypes, especially in plants, has become increasingly important. This chapter provides a detailed guide to the bioinformatics approach for the identification of transposon insertion polymorphisms (TIPs) using paired-end whole-genome sequencing data. Through the application of computational pipelines and validated methodologies, researchers can systematically identify and characterize TEs to investigate their roles in biological processes. We have outlined an approach that offers a robust and scalable framework for studying TE-driven genome evolution and its contributions to agronomic trait development, offering critical insights for foundational research and translational applications. This protocol leverages TRACKPOSON and complementary tools to identify genomic TEs and quantify TIPs in plants, including legumes.