On Hill et al's conjecture for calculating the subtree prune and regraft distance between phylogenies
Department of Computer Science, Technical University of Catalonia, Barcelona, Spain
BMC Evolutionary Biology 2010, 10:334 doi:10.1186/1471-2148-10-334Published: 29 October 2010
Recently, Hill et al.  implemented a new software package--called SPRIT--which aims at calculating the minimum number of horizontal gene transfer events that is needed to simultaneously explain the evolution of two rooted binary phylogenetic trees on the same set of taxa. To this end, SPRIT computes the closely related so-called rooted subtree prune and regraft distance between two phylogenies. However, calculating this distance is an NP-hard problem and exact algorithms are often only applicable to small- or medium-sized problem instances. Trying to overcome this problem, Hill et al. propose a divide-and-conquer approach to speed up their algorithm and conjecture that this approach can be used to compute the rooted subtree prune and regraft distance exactly.
In this note, we present a counterexample to Hill et al's conjecture and subsequently show that a modified version of their conjecture holds.
While Hill et al's conjecture may result in an overestimate of the rooted subtree prune and regraft distance, a slightly more restricted version of their approach gives the desired outcome and can be applied to speed up the exact calculation of this distance between two phylogenies.