Given two permutations σ and π, the Permutation Pattern problem asks if σ is a subpattern of π. We show that the problem can be solved in time 2 O( 2 log ) · n, where = |σ| and n = |π|. In other words, the problem is fixed-parameter tractable parameterized by the size of the subpattern to be found.We introduce a novel type of decompositions for permutations and a corresponding width measure. We present a linear-time algorithm that either finds σ as a subpattern of π, or finds a decomposition of π whose width is bounded by a function of |σ|. Then we show how to solve the Permutation Pattern problem in linear time if a bounded-width decomposition is given in the input.

a b s t r a c tWe study the parameterized complexity of several vertex-and edge-deletion problems on graphs, parameterized by the number p of deletions. The first kind of problems are separation problems on undirected graphs, where we aim at separating distinguished vertices in a graph. The second kind of problems are feedback set problems on group-labelled graphs, where we aim at breaking nonnull cycles in a graph having its arcs labelled by elements of a group. We obtain new FPT algorithms for these different problems, relying on a generic O * (4 p ) algorithm for breaking paths of a homogeneous path system.

This paper focuses on veto supertree methods; i.e., methods that aim at producing a conservative synthesis of the relationships agreed upon by all source trees. We propose desirable properties that a supertree should satisfy in this framework, namely the non-contradiction property (PC) and the induction property (PI). The former requires that the supertree does not contain relationships that contradict one or a combination of the source topologies, whereas the latter requires that all topological information contained in the supertree is present in a source tree or collectively induced by several source trees. We provide simple examples to illustrate their relevance and that allow a comparison with previously advocated properties. We show that these properties can be checked in polynomial time for any given rooted supertree. Moreover, we introduce the PhySIC method (PHYlogenetic Signal with Induction and non-Contradiction). For k input trees spanning a set of n taxa, this method produces a supertree that satisfies the above-mentioned properties in O(kn(3) + n(4)) computing time. The polytomies of the produced supertree are also tagged by labels indicating areas of conflict as well as those with insufficient overlap. As a whole, PhySIC enables the user to quickly summarize consensual information of a set of trees and localize groups of taxa for which the data require consolidation. Lastly, we illustrate the behaviour of PhySIC on primate data sets of various sizes, and propose a supertree covering 95% of all primate extant genera. The PhySIC algorithm is available at http://atgc.lirmm.fr/cgi-bin/PhySIC.