Jeremy M. Brown, Genevieve G. Mount, Kyle A. Gallivan, James Wilgenbusch

All phylogenetic studies are built around sets of trees. Tree sets carry different kinds of information depending on the data and approaches used to generate them, but ultimately the variation they contain and their structure is what drives new phylogenetic insights. In order to better understand the variation in and structure of phylogenetic tree sets, we need tools that are generic, flexible, and exploratory. These tools can serve as natural complements to more formal, statistical investigations and allow us to flag surprising or unexpected observations, better understand the results of model-based studies, as well as build intuition. Here, we describe such a set of tools and provide examples of how they can be applied to relevant questions in phylogenetics, phylogenomics, and species-tree inference. These tools include both visualization techniques and quantitative summaries and are currently implemented in the TreeScaper software package (Huang et al. 2016).