This document summarizes research on constructing a phylogenetic tree for COX genes using multiple sequence alignments with ClustalW. It begins by introducing phylogenetic analysis and the COX gene. It then describes the methodology used, which involved obtaining nucleotide sequences from a COX protein sequence in mice, performing a tBLASTn search to find related genes, aligning the sequences with ClustalW, and constructing rooted and unrooted phylogenetic trees. The results include the input protein sequence, tBLASTn output, ClustalW alignment, and the rooted and unrooted phylogenetic trees produced. It concludes that phylogenetic analysis is important for understanding gene and protein evolution.