The determination of a protein’s functional residues is key for understanding its function at the molecular level and devising ways of modifying it to our benefit. A plethora of computational methods exist for predicting these sites, and most of them make use of the information contained in a multiple sequence alignment of homologous proteins. Nowadays, these approaches are mature enough, both in terms of reliability and ease of use, to become part of the toolbox of any biologist. This chapter describes a simple protocol for generating a multiple sequence alignment for a protein of interest and detecting different types of functional positions on it, all using freely available web and desktop tools with graphical user interfaces.