With current trends in integrating phylogenetic analysis into pharma-research, Computing systems that integrate the two areas can help the drug discovery field. DrugTree is a tool that overlays ligand data on a protein-motivated phylogenetic tree. While initial tests of DrugTree are successful, it has been noticed that there are a number of lags concerning querying the tree. Due to the interleaving nature of the data, query optimization can become problematic since the data is being obtained from multiple sources, integrated and then presented to the user with the phylogenetic imposed upon the phylogenetic analysis layer. This poster presents our initial methodologies for addressing the query optimization issues. Our approach applies standards as well as uses novel mechanisms to help improve performance time.