Related papers: A 2-approximation algorithm for the softwired pars…
We propose a simple and natural approximation algorithm for the problem of finding a 2-edge-connected spanning subgraph of minimum total edge cost in a graph. The algorithm maintains a spanning forest starting with an empty edge set. In…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
We consider an incremental variant of the rooted prize-collecting Steiner-tree problem with a growing budget constraint. While no incremental solution exists that simultaneously approximates the optimum for all budgets, we show that a…
We examine a mathematical question concerning the reconstruction accuracy of the Fitch algorithm for reconstructing the ancestral sequence of the most recent common ancestor given a phylogenetic tree and sequence data for all taxa under…
We present approximation algorithms for the following NP-hard optimization problems related to bottleneck spanning trees in metric spaces. 1. The disjoint bottleneck spanning tree problem: Given $n$ pairs of points in a metric space, find…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the…
In a previous work, we gave a metric on the class of semibinary tree-sibling time consistent phylogenetic networks that is computable in polynomial time; in particular, the problem of deciding if two networks of this kind are isomorphic is…
Branchwidth determines how graphs, and more generally, arbitrary connectivity (basically symmetric and submodular) functions could be decomposed into a tree-like structure by specific cuts. We develop a general framework for designing…
Phylogenetic networks are a generalization of phylogenetic trees to leaf-labeled directed acyclic graphs that represent ancestral relationships between species whose past includes non-tree-like events such as hybridization and horizontal…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
We consider the $k$-prize-collecting Steiner tree problem. An instance is composed of an integer $k$ and a graph $G$ with costs on edges and penalties on vertices. The objective is to find a tree spanning at least $k$ vertices which…
Phylogenetic trees are frequently used to model evolution. Such trees are typically reconstructed from data like DNA, RNA, or protein alignments using methods based on criteria like maximum parsimony (amongst others). Maximum parsimony has…
Phylogenetic networks are a flexible model of evolution that can represent reticulate evolution and handle complex data. Tree-based networks, which are phylogenetic networks that have a spanning tree with the same root and leaf-set as the…
This paper studies the relationship between undirected (unrooted) and directed (rooted) phylogenetic networks. We describe a polynomial-time algorithm for deciding whether an undirected nonbinary phylogenetic network, given the locations of…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
The maximum common subtree isomorphism problem asks for the largest possible isomorphism between subtrees of two given input trees. This problem is a natural restriction of the maximum common subgraph problem, which is ${\sf NP}$-hard in…
We study a core algorithmic problem in network design called ${F}$-augmentation that involves increasing the connectivity of a given family of cuts ${F}$. Over 30 years ago, Williamson et al. (STOC `93) provided a 2-approximation…
Causal Bayesian networks are widely used tools for summarising the dependencies between variables and elucidating their putative causal relationships. By restricting the search to trees, for example, learning the optimum from data is…
In Polyamorous Scheduling, we are given an edge-weighted graph and must find a periodic schedule of matchings in this graph which minimizes the maximal weighted waiting time between consecutive occurrences of the same edge. This NP-hard…
We present the first fixed-parameter algorithm for constructing a tree-child phylogenetic network that displays an arbitrary number of binary input trees and has the minimum number of reticulations among all such networks. The algorithm…