The lack of simple methods to identify relevant T-cell epitopes, the high mutation rate of many pathogens, and restriction of T-cell response to epitopes due to human lymphocyte antigen (HLA) polymorphism have significantly hindered the development of cytotoxic T-lymphocyte (CTL) epitope-based or "epitope-driven" vaccines. Previously, CTL epitopes were mapped using large arrays of overlapping synthetic peptides. The large number of protein sequences available for mapping is now making this method prohibitively expensive and time-consuming. Bioinformatics tools such as EpiMatrix and Conservatrix, which search for unique or multi-HLA-restricted (promiscuous) T-cell epitopes and identify epitopes that are conserved across variant strains of the same pathogen, accelerate epitope mapping. These tools offer a significant advantage over other methods of epitope selection because high-throughput screening can be performed in silico, followed by confirmatory studies in vitro. CTL epitopes discovered using these tools might be used to develop novel vaccines and therapeutics for the prevention and treatment of infectious diseases such as human immunodeficiency virus, hepatitis C, tuberculosis, and some cancers.