Related papers: Representing Partitions on Trees
Phylogenetic networks are a special type of graph which generalize phylogenetic trees and that are used to model non-treelike evolutionary processes such as recombination and hybridization. In this paper, we consider {\em unrooted}…
Recently, the minimum number of reticulation events that is required to simultaneously embed a collection P of rooted binary phylogenetic trees into a so-called temporal network has been characterized in terms of cherry-picking sequences.…
The question whether a partition $\mathcal{P}$ and a hierarchy $\mathcal{H}$ or a tree-like split system $\mathfrak{S}$ are compatible naturally arises in a wide range of classification problems. In the setting of phylogenetic trees, one…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
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…
In 1989 Erd\H{o}s and Sz\'ekely showed that there is a bijection between (i) the set of rooted trees with $n+1$ vertices whose leaves are bijectively labeled with the elements of $[\ell]=\{1,2,\dots,\ell\}$ for some $\ell \leq n$, and (ii)…
It is well-known that the Vertex Cover problem is in P on bipartite graphs, however; the computational complexity of the Partial Vertex Cover problem on bipartite graphs is open. In this paper, we first show that the Partial Vertex Cover…
The perfect phylogeny problem is a classic problem in computational biology, where we seek an unrooted phylogeny that is compatible with a set of qualitative characters. Such a tree exists precisely when an intersection graph associated…
In phylogenetics, tree-based networks are used to model and visualize the evolutionary history of species where reticulate events such as horizontal gene transfer have occurred. Formally, a tree-based network $N$ consists of a phylogenetic…
The evolutionary relationships among organisms have traditionally been represented using rooted phylogenetic trees. However, due to reticulate processes such as hybridization or lateral gene transfer, evolution cannot always be adequately…
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…
We consider a variant of treewidth that we call clique-partitioned treewidth in which each bag is partitioned into cliques. This is motivated by the recent development of FPT-algorithms based on similar parameters for various problems. With…
A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…
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…
Phylogenetic networks generalize phylogenetic trees by representing reticulate evolution. Tree-based networks and their support trees have been extensively studied, but not all networks are tree-based. To measure how far such networks are…
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…
Tree-based priors for probability distributions are usually specified using a predetermined, data-independent collection of candidate recursive partitions of the sample space. To characterize an unknown target density in detail over the…
Methods for detecting community structure in networks typically aim to identify a single best partition of network nodes into communities, often by optimizing some objective function, but in real-world applications there may be many…
We consider partitions of a point set into two parts, and the lengths of the minimum spanning trees of the original set and of the two parts. If $w(P)$ denotes the length of a minimum spanning tree of $P$, we show that every set $P$ of $n…
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 $X$…