This article provides a detailed protocol for building phylogenetic trees from molecular data using the software MEGA5. The process is divided into four main steps: identifying and acquiring homologous sequences, aligning those sequences, constructing a phylogenetic tree, and presenting the tree. MEGA5 is highlighted as an integrated program that simplifies these steps by offering a single user interface and eliminating the need to convert file formats between different programs. The article covers the use of BLAST for sequence identification, alignment methods (ClustalW and MUSCLE), maximum likelihood tree construction, and tree visualization. It also discusses the importance of choosing appropriate substitution models and the reliability of the tree through bootstrapping. Additionally, the article provides alternatives to MEGA5 for each step, such as using NCBI BLAST, text editors for sequence editing, and other tree-drawing programs like PhyML and FigTree. The article emphasizes the importance of correctly presenting the tree, including the correct format (unrooted or rooted) and the use of appropriate legends to avoid misinterpretation.This article provides a detailed protocol for building phylogenetic trees from molecular data using the software MEGA5. The process is divided into four main steps: identifying and acquiring homologous sequences, aligning those sequences, constructing a phylogenetic tree, and presenting the tree. MEGA5 is highlighted as an integrated program that simplifies these steps by offering a single user interface and eliminating the need to convert file formats between different programs. The article covers the use of BLAST for sequence identification, alignment methods (ClustalW and MUSCLE), maximum likelihood tree construction, and tree visualization. It also discusses the importance of choosing appropriate substitution models and the reliability of the tree through bootstrapping. Additionally, the article provides alternatives to MEGA5 for each step, such as using NCBI BLAST, text editors for sequence editing, and other tree-drawing programs like PhyML and FigTree. The article emphasizes the importance of correctly presenting the tree, including the correct format (unrooted or rooted) and the use of appropriate legends to avoid misinterpretation.