Allows the user to identify subfamily determining sites (SDS) within a protein family. SubSite takes two different approaches to identify a SDS site. At first SubSite estimates the average relative conservancy of each amino acid residues in the subgroups of the protein family through a hypothetical mutational approach. SubSite next categorizes the sequence alignment columns based on their compositional complexity. Given a protein sequence alignment and its subfamily division information, SubSite predicts the potential subfamily determining sites using the above mentioned approaches.