The availability of collections of genome-wide deletion mutants greatly accelerates systematic analyses of gene function. However, each of the thousands of genes that comprise a genome must be phenotyped individually unless they can be assayed in parallel and subsequently deconvolved. To this end, unique molecular identifiers have been developed for a variety of microbes. Specifically, the addition of DNA "tags," or "bar codes," to each mutant allows all mutants in a collection to be pooled and phenotyped in parallel, greatly increasing experimental throughput. In this chapter, we provide an overview of current methodologies used to create such tagged mutant collections and outline how they can be applied to understand gene function, gene-gene interactions, and drug-gene interactions. Finally, we present a methodology that uses universal TagModules, capable of bar coding a wide range of microorganisms, and demonstrate its reduction to practice by creating tagged mutant collections in the pathogenic yeast Candida albicans.