Chemical Graph theory is used to model physical properties of molecules called alkanes. Indices based on the graphical structure of the alkanes are defined and used to model both the boiling point and melting point of the molecules. The predictive ability of these models and their errors are presented in several graphs and tables. Java applets allow for interactive exploration of the alkanes. A student project based on this research and a discussion of its application are included, along with spreadsheets of model data.