For many undergraduates, one of the most challenging exercises in the study of evolutionary biology is developing and testing evolutionary hypotheses using phylogenetic trees. In this series of modules, modified from Kleinschmit et al. (2019), students develop predictions about tree structure under different evolutionary hypotheses, and assemble data from FASTA-formatted sequence files and databases hosted by NCBI (The National Center for Biotechnology Information). They then use the free, user-friendly program MEGA X to align sequence data and construct simple trees to test their hypotheses. These modules cover a key learning objective in biology—application of bioinformatics tools to answer a real-life biological question. Specifically, they allow students the opportunity to combine their knowledge of tree-thinking, skills in database searching (NCBI), and experience in making phylogenies (MEGA) to answer inquiry-based research questions on a range of applied topics.