EMPeror is an interactive next generation tool for the analysis, visualization and understanding of high throughput microbial ecology datasets. Due to its tailor-made graphical user interface, delving into a new dataset to elucidate the patterns hidden in the data has never been easier. EMPeror brings a rich set of customizations and modifications that can be integrated into any QIIME compliant dataset; with lightweight data files and hardware accelerated graphics, constitutes itself as the state of the art for analyzing N-dimensional data using principal coordinates analysis. Yoshiki Vazquez-Baeza, Meg Pirrung, Antonio Gonzalez, Rob Knight; Gigascience, 2013; doi: 10.1186/2047-217X-2-16.