A Cubic-Vertex Kernel for Flip Consensus Tree

Abstract

Given a bipartite graph G=(V_c,V_t,E) and a non-negative integer k, the NP-complete Minimum-Flip Consensus Tree problem asks whether G can be transformed, using up to k edge insertions and deletions, into a graph that does not contain an induced P_5 with its first vertex in V_t (a so-called M-graph or Sigma-graph). This problem plays an important role in computational phylogenetics, V_c standing for the characters and V_t standing for taxa. Chen et al. [IEEE/ACM TCBB 2006] showed that Minimum-Flip Consensus Tree is NP-complete and presented a parameterized algorithm with running time O(6^k\cdot |V_t|\cdot |V_c|). Recently, Boecker et al. [IWPEC'08] presented a refined search tree algorithm with running time O(4.83^k(|V_t|+|V_c|) + |V_t|\cdot |V_c|). We complement these results by polynomial-time executable data reduction rules yielding a problem kernel with O(k^3) vertices.