On retracts, absolute retracts, and folds in cographs

Let G and H be two cographs. We show that the problem to determine whether H is a retract of G is NP-complete. We show that this problem is fixed-parameter tractable when parameterized by the size of H. When restricted to the class of threshold graphs or to the class of trivially perfect graphs, the problem becomes tractable in polynomial time. The problem is also soluble when one cograph is given as an induced subgraph of the other. We characterize absolute retracts of cographs.Comment: 15 page

Limits of Structures and the Example of Tree-Semilattices

The notion of left convergent sequences of graphs introduced by Lov\' asz et al. (in relation with homomorphism densities for fixed patterns and Szemer\'edi's regularity lemma) got increasingly studied over the past $10$ years. Recently, Ne\v set\v ril and Ossona de Mendez introduced a general framework for convergence of sequences of structures. In particular, the authors introduced the notion of $QF$-convergence, which is a natural generalization of left-convergence. In this paper, we initiate study of $QF$-convergence for structures with functional symbols by focusing on the particular case of tree semi-lattices. We fully characterize the limit objects and give an application to the study of left convergence of $m$-partite cographs, a generalization of cographs

Partial Homology Relations - Satisfiability in terms of Di-Cographs

Directed cographs (di-cographs) play a crucial role in the reconstruction of evolutionary histories of genes based on homology relations which are binary relations between genes. A variety of methods based on pairwise sequence comparisons can be used to infer such homology relations (e.g.\ orthology, paralogy, xenology). They are \emph{satisfiable} if the relations can be explained by an event-labeled gene tree, i.e., they can simultaneously co-exist in an evolutionary history of the underlying genes. Every gene tree is equivalently interpreted as a so-called cotree that entirely encodes the structure of a di-cograph. Thus, satisfiable homology relations must necessarily form a di-cograph. The inferred homology relations might not cover each pair of genes and thus, provide only partial knowledge on the full set of homology relations. Moreover, for particular pairs of genes, it might be known with a high degree of certainty that they are not orthologs (resp.\ paralogs, xenologs) which yields forbidden pairs of genes. Motivated by this observation, we characterize (partial) satisfiable homology relations with or without forbidden gene pairs, provide a quadratic-time algorithm for their recognition and for the computation of a cotree that explains the given relations