Phylogentic analyses are gradually reaching genomic scales. Nowadays, many resources and surveys encompass a large number of trees that, often, cannot be manually analyzed. Bioinformatics toolkits are intended to provide a flexible framework to deal with specific data in a programmatic way, thus facilitating the analysis of large collections of data. The Environment for Tree Exploration (ETE, http://ete.cgenomics.org) is a Python programming toolkit specially focused on dealing with hierarchical trees. It allows, for instance, to perform a number of operations on phylogenetic trees, as well as designing automatic pipelines. It also provides a highly customizable drawing engine, which can be used to create complex annotated tree images in an automatic way or to interactively explore single trees. Moreover, the ETE toolkit is not only limited to large scale analyses, as it can be used to easily develop specific tree analysis methods for single trees.