Related papers: Solving the Tree Containment Problem Using Graph N…
Phylogenetic networks represent evolutionary history of species and can record natural reticulate evolutionary processes such as horizontal gene transfer and gene recombination. This makes phylogenetic networks a more comprehensive…
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…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
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…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Galled trees are studied as a recombination model in theoretic population genetics. This class of phylogenetic networks has been generalized to tree-child networks, normal networks and tree-based networks by relaxing a structural condition.…
Rooted acyclic graphs appear naturally when the phylogenetic relationship of a set $X$ of taxa involves not only speciations but also recombination, horizontal transfer, or hybridization, that cannot be captured by trees. A variety of…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Given a $\{0,1\}$-matrix $M$, the graph realization problem for $M$ asks if there exists a spanning forest such that the columns of $M$ are incidence vectors of paths in the forest. The problem is closely related to the recognition of…
The supertree problem asking for a tree displaying a set of consistent input trees has been largely considered for the reconstruction of species trees. Here, we rather explore this framework for the sake of reconstructing a gene tree from a…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
We study the problem of visualizing phylogenetic networks, which are extensions of the Tree of Life in biology. We use a space filling visualization method, called DAGmaps, in order to obtain clear visualizations using limited space. In…
Tree-child networks are a recently-described class of directed acyclic graphs that have risen to prominence in phylogenetics (the study of evolutionary trees and networks). Although these networks have a number of attractive mathematical…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…
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…
In the Fully Leafed Induced Subtrees, one is given a graph $G$ and two integers $a$ and $b$ and the question is to find an induced subtree of $G$ with $a$ vertices and at least $b$ leaves. This problem is known to be NP-complete even when…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
The Steiner tree problem aims to determine a minimum edge-weighted tree that spans a given set of terminal vertices from a given graph. In the past decade, a considerable number of algorithms have been developed to solve this…
We study the problem of connecting the parts of a multipartite graph using a minimum number of edges under a matching constraint. We introduce interconnection trees, defined as matchings whose projections onto the quotient graph form a…