Algorithmic Aspects of Switch Cographs

This paper introduces the notion of involution module, the first generalization of the modular decomposition of 2-structure which has a unique linear-sized decomposition tree. We derive an O(n^2) decomposition algorithm and we take advantage of the involution modular decomposition tree to state several algorithmic results. Cographs are the graphs that are totally decomposable w.r.t modular decomposition. In a similar way, we introduce the class of switch cographs, the class of graphs that are totally decomposable w.r.t involution modular decomposition. This class generalizes the class of cographs and is exactly the class of (Bull, Gem, Co-Gem, C_5)-free graphs. We use our new decomposition tool to design three practical algorithms for the maximum cut, vertex cover and vertex separator problems. The complexity of these problems was still unknown for this class of graphs. This paper also improves the complexity of the maximum clique, the maximum independant set, the chromatic number and the maximum clique cover problems by giving efficient algorithms, thanks to the decomposition tree. Eventually, we show that this class of graphs has Clique-Width at most 4 and that a Clique-Width expression can be computed in linear time

Independent sets of maximum weight in apple-free graphs

We present the first polynomial-time algorithm to solve the maximum weight independent set problem for apple-free graphs, which is a common generalization of several important classes where the problem can be solved efficiently, such as claw-free graphs, chordal graphs, and cographs. Our solution is based on a combination of two algorithmic techniques (modular decomposition and decomposition by clique separators) and a deep combinatorial analysis of the structure of apple-free graphs. Our algorithm is robust in the sense that it does not require the input graph G to be apple-free; the algorithm either finds an independent set of maximum weight in G or reports that G is not apple-free

A Fast Parallel Algorithm to Recognize P4-Sparse Graphs

A number of problems in mobile computing, group-based collaboration, automated theorem proving, networking, scheduling, and cluster analysis suggested the study of graphs featuring certain “local density” characteristics. Typically, the notion of local density is equated with the absence of chordless paths of length three or more. Recently, a new metric for local density has been proposed, allowing a number of such induced paths to occur. More precisely, a graphG is called P4-sparse if no set of five vertices inG induces more than one chordless path of length three. P4-sparse graphs generalize the well-known class of cographs corresponding to a more stringent local density metric. One remarkable feature of P4-sparse graphs is that they admit a tree representation unique up to isomorphism. In this work we present a parallel algorithm to recognize P4-sparse graphs and show how the data structures returned by the recognition algorithm can be used to construct the corresponding tree representation. With a graphG= (V, E) with¦V¦=n and¦E¦= m as input, our algorithms run inO(log n) time usingO((n2 + mn)/ log n) processors in the EREW-PRAM model

Phylogenetics from paralogs

Motivation: Sequence-based phylogenetic approaches heavily rely on initial data sets to be composed of orthologous sequences only. Paralogs are treated as a dangerous nuisance that has to be detected and removed. Recent advances in mathematical phylogenetics, however, have indicated that gene duplications can also convey meaningful phylogenetic information provided orthologs and paralogs can be distinguished with a degree of certainty. Results: We demonstrate that plausible phylogenetic trees can be inferred from paralogy information only. To this end, tree-free estimates of orthology, the complement of paralogy, are first corrected to conform cographs and then translated into equivalent event-labeled gene phylogenies. A certain subset of the triples displayed by these trees translates into constraints on the species trees. While the resolution is very poor for individual gene families, we observe that genome-wide data sets are sufficient to generate fully resolved phylogenetic trees of several groups of eubacteria. The novel method introduced here relies on solving three intertwined NP-hard optimization problems: the cograph editing problem, the maximum consistent triple set problem, and the least resolved tree problem. Implemented as Integer Linear Program, paralogy-based phylogenies can be computed exactly for up to some twenty species and their complete protein complements. Availability:The ILP formulation is implemented in the Software ParaPhylo using IBM ILOG CPLEX (TM) Optimizer 12.6 and is freely available from http://pacosy.informatik.uni-leipzig.de/paraphyl

On the p-Connectedness of Graphs – a Survey

A graph is said to be p-connected if for every partition of its vertices into two non-empty, disjoint, sets some chordless path with three edges contains vertices from both sets in the partition. As it turns out, p-connectedness generalizes the usual connectedness of graphs and leads, in a natural way, to a unique tree representation for arbitrary graphs. This paper reviews old and new results, both structural and algorithmic, about p-connectedness along with applications to various graph decompositions