A new method for determining functionally important protein residues is analyzed and compared with two previously existing methods. This thesis presents the analysis of several different protein sequences and shows how the functionally important protein residues compare between the evolutionary trace method, the maximum likelihood method of protein evolution, and the Hidden Markov method of protein evolution. The results are presented graphically as well as structurally since structure information is known about all the protein sequences studied. All three methods produce similar results for most of the proteins and show that the most highly conserved protein residues are detectable by all three methods but that the less conserved important residues may not always be identified by all methods.