Related papers: Computing Rooted and Unrooted Maximum Consistent S…
We present a new universal source code for distributions of unlabeled binary and ordinal trees that achieves optimal compression to within lower order terms for all tree sources covered by existing universal codes. At the same time, it…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
We present an efficient algorithm to compute permanents, mixed discriminants and hyperdeterminants of structured matrices and multidimensional arrays (tensors). We describe the sparsity structure of an array in terms of a graph, and we…
It is known that the size of the largest common subtree (i.e., the maximum agreement subtree) of two independent random binary trees with $n$ given labeled leaves is of order between $n^{0.366}$ and $n^{1/2}$. We improve the lower bound to…
A monotone drawing of a graph G is a straight-line drawing of G such that every pair of vertices is connected by a path that is monotone with respect to some direction. Trees, as a special class of graphs, have been the focus of several…
There are multiple factors which can cause the phylogenetic inference process to produce two or more conflicting hypotheses of the evolutionary history of a set X of biological entities. That is: phylogenetic trees with the same set of leaf…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Given a rooted point set $P$, the rooted $y-$Monotone Minimum Spanning Tree (rooted $y-$MMST) of $P$ is the spanning geometric graph of $P$ in which all the vertices are connected to the root by some $y-$monotone path and the sum of the…
Designing well-connected graphs is a fundamental problem that frequently arises in various contexts across science and engineering. The weighted number of spanning trees, as a connectivity measure, emerges in numerous problems and plays a…
Recently, considerable effort has been put into developing fast algorithms to reconstruct a rooted phylogenetic network that explains two rooted phylogenetic trees and has a minimum number of hybridization vertices. With the standard…
We consider the counting problem of the number of \textit{leaf-labeled increasing trees}, where internal nodes may have an arbitrary number of descendants. The set of all such trees is a discrete representation of the genealogies obtained…
An important and well-studied problem in phylogenetics is to compute a \emph{consensus tree} so as to summarize the common features within a collection of rooted phylogenetic trees, all whose leaf-sets are bijectively labeled by the same…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
Search trees on trees (STTs) generalize the fundamental binary search tree (BST) data structure: in STTs the underlying search space is an arbitrary tree, whereas in BSTs it is a path. An optimal BST of size $n$ can be computed for a given…
A tree-based network on a set $X$ of $n$ leaves is said to be universal if any rooted binary phylogenetic tree on $X$ can be its base tree. Francis and Steel showed that there is a universal tree-based network on $X$ in the case of $n=3$,…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Let $\mathcal{O}_n$ be the set of ordered labeled trees on ${0,...,n}$. A maximal decreasing subtree of an ordered labeled tree is defined by the maximal ordered subtree from the root with all edges being decreasing. In this paper, we study…
In this paper, we investigate a problem concerning quartets, which are a particular type of tree on four leaves. Loosely speaking, a set of quartets is said to be `definitive' if it completely encapsulates the structure of some larger tree,…
Supertree methods are tree reconstruction techniques that combine several smaller gene trees (possibly on different sets of species) to build a larger species tree. The question of interest is whether the reconstructed supertree converges…
Let $G$ be a simple graph on $n$ vertices. We consider the problem LIS of deciding whether there exists an induced subtree with exactly $i \leq n$ vertices and $\ell$ leaves in $G$. We study the associated optimization problem, that…