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README.md

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 ## What is ARETE?
 
-**ARETE** is a bioinformatics best-practice analysis pipeline for profiling the **genomic repertoire** and **evolutionary dynamics** of microorganisms with a particular focus on pathogens. We use ARETE is to identify important genes (e.g., those that confer antimicrobial resistance or contribute to virulence) and mobile genetic elements such as plasmids and genomic islands, and infer important routes by which these are transmitted using evidence from recombination, coevolution, and phylogenetic tree comparisons.
+**ARETE** (Antmicrobial Resistance: Emergence, Transmission, and Ecology) is a bioinformatics best-practice analysis pipeline for profiling the **genomic repertoire** and **evolutionary dynamics** of microorganisms with a particular focus on pathogens. We use ARETE is to identify important genes (e.g., those that confer antimicrobial resistance or contribute to virulence) and mobile genetic elements such as plasmids and genomic islands, and infer important routes by which these are transmitted using evidence from recombination, coevolution, and phylogenetic tree comparisons.
 
 ARETE produces a range of useful outputs, including those generated by each tool integrated into the pipeline, as well as summaries across the entire dataset such as phylogenetic profiles. Outputs from ARETE can also be fed into packages such as Coeus and MicroReact. Although ARETE was primarily developed with pathogens in mind, inference of pan-genomes, mobilomes, and phylogenomic histories can be performed for any set of microbial genomes, with the proviso that reference databases are much more complete for some groups than others! The tools in ARETE work best at the species and genus level of relatedness.