Related papers: A 2-approximation algorithm for the softwired pars…
Given a graph G, the {\em maximum internal spanning tree problem} (MIST for short) asks for computing a spanning tree T of G such that the number of internal vertices in T is maximized. MIST has possible applications in the design of…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Rooted phylogenetic networks are often used to represent conflicting phylogenetic signals. Given a set of clusters, a network is said to represent these clusters in the "softwired" sense if, for each cluster in the input set, at least one…
We study the problem of maintaining a breadth-first spanning tree (BFS tree) in partially dynamic distributed networks modeling a sequence of either failures or additions of communication links (but not both). We present deterministic…
It has remained an open question for some time whether, given a set of not necessarily binary (i.e. "nonbinary") trees T on a set of taxa X, it is possible to determine in time f(r).poly(m) whether there exists a phylogenetic network that…
Computing an optimal classification tree that provably maximizes training performance within a given size limit, is NP-hard, and in practice, most state-of-the-art methods do not scale beyond computing optimal trees of depth three.…
The Maximum Agreement Forest problem has been extensively studied in phylogenetics. Most previous work is on two binary phylogenetic trees. In this paper, we study a generalized version of the problem: the Maximum Agreement Forest problem…
In this experimental study we consider Steiner tree approximations that guarantee a constant approximation of ratio smaller than $2$. The considered greedy algorithms and approaches based on linear programming involve the incorporation of…
Constrained forest problems form a class of graph problems where specific connectivity requirements for certain cuts within the graph must be satisfied by selecting the minimum-cost set of edges. The prize-collecting version of these…
Phylogenetic (i.e. leaf-labeled) trees play a fundamental role in evolutionary research. A typical problem is to reconstruct such trees from data like DNA alignments (whose columns are often referred to as characters), and a simple…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
An evolutionary tree (phylogenetic tree) is a binary, rooted, unordered tree that models the evolutionary history of currently living species in which leaves are labeled by species. In this paper, we investigate the problem of finding the…
Evolutionary scenarios displaying reticulation events are often represented by rooted phylogenetic networks. Due to biological reasons, those events occur very rarely, and, thus, networks containing a minimum number of such events,…
Several algorithms build on the perfect phylogeny model to infer evolutionary trees. This problem is particularly hard when evolutionary trees are inferred from the fraction of genomes that have mutations in different positions, across…
A \emph{binary tanglegram} is a drawing of a pair of rooted binary trees whose leaf sets are in one-to-one correspondence; matching leaves are connected by inter-tree edges. For applications, for example, in phylogenetics, it is essential…
In phylogenetics, phylogenetic trees are rooted binary trees, whereas phylogenetic networks are rooted arbitrary acyclic digraphs. Edges are directed away from the root and leaves are uniquely labeled with taxa in phylogenetic networks. For…
Phylogenetic trees are used to model evolution: leaves are labelled to represent contemporary species ("taxa") and interior vertices represent extinct ancestors. Informally, convex characters are measurements on the contemporary species in…
Determining the interaction partners among protein/domain families poses hard computational problems, in particular in the presence of paralogous proteins. Available approaches aim to identify interaction partners among protein/domain…
Given a directed graph $G$ on $n$ vertices with a special vertex $s$, the directed minimum degree spanning tree problem requires computing a incoming spanning tree rooted at $s$ whose maximum tree in-degree is the smallest among all such…
We address an open question of Francis and Steel about phylogenetic networks and trees. They give a polynomial time algorithm to decide if a phylogenetic network, N, is tree-based and pose the problem: given a fixed tree T and network N, is…