In this chapter, we will use sequences of your aoi gene family from multiple species of bacteria to build a phylogenetic tree, and compare the tree made based on these sequences to the known taxonomy of bacteria. In a real study, we would use the nucleotide sequence of the genes, but for simplicity, we will use the protein sequences in this lab. Protein sequences are easier to unambiguously align, and we don’t have to worry about red herrings such as differences in GC content. This makes the construction of the tree simpler. We will use a distance-based method for tree construction. When the sequences are closer in the tree than their host bacterial species, it is good evidence for horizontal gene transfer. Students are expected to explain why antibiotics resistance is a severe problem by comparing the tree.