Parameterized enumeration, transversals, and imperfect phylogeny reconstruction

Journal article, 2006

We study parameterized enumeration problems where we are interested in all solutions of limited size rather than just some solution of minimum cardinality. (Actually, we have to enumerate the inclusion-minimal solutions in order to get FPT results.) Two novel concepts are the notion of a full kernel that contains all small solutions and implicit enumeration of solutions in form of compressed descriptions. In particular, we study combinatorial and computational bounds for the transversal hypergraph (vertex covers in graphs is a special case), restricted to hyperedges with at most k elements. As an example, we apply the results and further special-purpose techniques to almost-perfect phylogeny reconstruction, a problem in in computational biology.