Related papers: Compatibility of Partitions with Trees, Hierarchie…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
A split system on a multiset $\mathcal M$ is a set of bipartitions of $\mathcal M$. Such a split system $\mathfrak S$ is compatible if it can be represented by a tree in such a way that the vertices of the tree are labelled by the elements…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
Given a tree $T$ on $n$ vertices, and $k, b, s_1, \ldots, s_b \in N$, the Tree Partitioning problem asks if at most $k$ edges can be removed from $T$ so that the resulting components can be grouped into $b$ groups such that the number of…
Deciding whether a collection of unrooted trees is compatible is a fundamental problem in phylogenetics. Two different graph-theoretic characterizations of tree compatibility have recently been proposed. In one of these, tree compatibility…
Compatibility of unrooted phylogenetic trees is a well studied problem in phylogenetics. It asks to determine whether for a set of k input trees there exists a larger tree (called a supertree) that contains the topologies of all k input…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Trigraph list homomorphism problems (also known as list matrix partition problems) have generated recent interest, partly because there are concrete problems that are not known to be polynomial time solvable or NP-complete. Thus while…
In this paper, we study three algorithmic problems involving computation trees: the optimization, solvability, and satisfiability problems. The solvability problem is concerned with recognizing computation trees that solve problems. The…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Matchings and coverings are central topics in graph theory. The close relationship between these two has been key to many fundamental algorithmic and polyhedral results. For mixed graphs, the notion of matching forest was proposed as a…
A hierarchy on a set $S$, also called a total partition of $S$, is a collection $\mathcal{H}$ of subsets of $S$ such that $S \in \mathcal{H}$, each singleton subset of $S$ belongs to $\mathcal{H}$, and if $A, B \in \mathcal{H}$ then $A \cap…
We show that P2T - the problem of deciding whether the edge set of a simple graph can be partitioned into two trees or not - is NP-complete.
Background: Tree reconciliation problems have long been studied in phylogenetics. A particular variant of the reconciliation problem for a gene tree T and a species tree S assumes that for each interior vertex x of T it is known whether x…
In a supercritical branching particle system, the trimmed tree consists of those particles which have descendants at all times. We develop this concept in the superprocess setting. For a class of continuous superprocesses with Feller…
A classical problem in phylogenetic tree analysis is to decide whether there is a phylogenetic tree $T$ that contains all information of a given collection $\cP$ of phylogenetic trees. If the answer is "yes" we say that $\cP$ is compatible…
A widely used method for determining the similarity of two labeled trees is to compute a maximum agreement subtree of the two trees. Previous work on this similarity measure is only concerned with the comparison of labeled trees of two…
A trigraph is a graph where each pair of vertices is labelled either 0 (a non-arc), 1 (an arc) or $\star$ (both an arc and a non-arc). In a series of papers, Hell and co-authors proposed to study the complexity of homomorphisms from graphs…
In evolutionary biology, biologists often face the problem of constructing a phylogenetic tree on a set $X$ of species from a multiset $\Pi$ of partitions corresponding to various attributes of these species. One approach that is used to…