Intractability of the Minimum-Flip Supertree problem and its variants

Abstract: Computing supertrees is a central problem in phylogenetics. The supertree method that is by far the most widely used today was introduced in 1992 and is called Matrix Representation with Parsimony analysis (MRP). Matrix Representation using Flipping (MRF)}, which was introduced in 2002, is an interesting variant of MRP: MRF is arguably more relevant that MRP and various efficient implementations of MRF have been presented. From a theoretical point of view, implementing MRF or MRP is solving NP-hard optimization problems. The aim of this paper is to study the approximability and the fixed-parameter tractability of the optimization problem corresponding to MRF, namely Minimum-Flip Supertree. We prove strongly negative results.