The work of this proposed project is a unique study of how transmembrane proteins and extra-membrane proteins may produce model misspecification. We examine transmembrane proteins and how the models of sequence evolution for the transmembrane regions differ from those for extra membrane sites. The transmembrane and extra membrane sites in transmembrane proteins are known to have different amino acid compositions. Previous research has shown that they exhibit different patterns of sequence evolution and even nearly significant topological distances (i.e., had they been significant the analyses would have produced trees that imply different taxonomies). We hypothesize an expanded sample size will allow us to detect a significant difference.