A faster fixed-parameter approach to drawing binary tanglegrams

Abstract

Given two binary phylogenetic trees covering the same n species, it is useful to compare them by drawing them with leaves arranged side-by-side. To facilitate comparison, we would like to arrange the trees to minimize the number of crossings k induced by connecting pairs of identical species. This is the NP-hard Tanglegram Layout problem. By providing a fast transformation to the Balanced Subgraph problem, we show that the problem admits an O(2 kn4) algorithm, improving upon a previous fixed-parameter approach with running time O(cknO(1)) where c ≈ 1000. We enhance a Balanced Subgraph implementation based on data reduction and iterative compression with improvements tailored towards these instances, and run experiments with real-world data to show the practical applicability of this approach. All practically relevant (k ≤ 1000) Tanglegram Layout instances can be solved exactly within seconds. Additionally, we provide a kernel-like bound by showing how to reduce the Balanced Subgraph instances for Tanglegram Layout on complete binary trees to a size of O(k logk). © 2009 Springer-Verlag.