Phylogenetics, or reconstructing the evolutionary relationships of organisms, is critical for understanding evolution. A large number of heuristic algorithms for phylogenetics have been developed, some of which enable estimates of trees with tens of thousands of taxa. Such trees may not be robust, as small changes in the input data can cause major differences in the optimal topology. Tools that can assess the quality and stability of phylogenetic tree estimates and identify the most reliable parts of the tree are needed.