Protein sequence analysis has been utilized to explore features of protein structure, protein interactions, and enzyme mechanism. One approach is to compare sequences using multiple sequence alignment (MSA) and identify relationships or interdependencies within a protein sequence. This chapter will describe the Protein Sequence Interdependency Calculator (PSICalc) software tool. PSICalc is a GUI tool for analyzing protein MSAs to identify sequence interdependencies using a K modes algorithm approach. The software outputs information about sequence clusters both in graphical and in CSV format. In addition, the tool identifies sites that are invariant and nearly invariant within a group of sequences. Finally, the tool also has the ability to compare separate MSAs of two or more proteins to identify interdependencies between or among proteins.