Related papers: On the maximum quartet distance between phylogenet…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…
We derive Singleton-type bounds on the free distance and column distances of trellis codes. Our results show that, at a given time instant, the maximum attainable column distance of trellis codes can exceed that of convolutional codes.…
We study the number of distance queries needed to identify certain properties of a hidden tree $T$ on $n$ vertices. A distance query consists of two vertices $x,y$, and the answer is the distance of $x$ and $y$ in $T$. We determine the…
The burning number is a recently introduced graph parameter indicating the spreading speed of content in a graph through its edges. While the conjectured upper bound on the necessary numbers of time steps until all vertices are reached is…
The aim of rendezvous in a graph is meeting of two mobile agents at some node of an unknown anonymous connected graph. In this paper, we focus on rendezvous in trees, and, analogously to the efforts that have been made for solving the…
We study the problem of how well a tree metric is able to preserve the sum of pairwise distances of an arbitrary metric. This problem is closely related to low-stretch metric embeddings and is interesting by its own flavor from the line of…
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have…
In this article we study the treewidth of the \emph{display graph}, an auxiliary graph structure obtained from the fusion of phylogenetic (i.e., evolutionary) trees at their leaves. Earlier work has shown that the treewidth of the display…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
A tanglegram $\cal T$ consists of two rooted binary trees with the same number of leaves, and a perfect matching between the two leaf sets. In a layout, the tanglegrams is drawn with the leaves on two parallel lines, the trees on either…
In 2001 Allen and Steel showed that, if subtree and chain reduction rules have been applied to two unrooted phylogenetic trees, the reduced trees will have at most 28k taxa where k is the TBR (Tree Bisection and Reconnection) distance…
A subtree of a tree is any induced subgraph that is again a tree (i.e., connected). The mean subtree order of a tree is the average number of vertices of its subtrees. This invariant was first analyzed in the 1980s by Jamison. An intriguing…
We present an algorithm for computing a maximum agreement subtree of two unrooted evolutionary trees. It takes O(n^{1.5} log n) time for trees with unbounded degrees, matching the best known time complexity for the rooted case. Our…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
A code $\mathcal{C} \subseteq \{0, 1, 2\}^n$ is said to be trifferent with length $n$ when for any three distinct elements of $\mathcal{C}$ there exists a coordinate in which they all differ. Defining $\mathcal{T}(n)$ as the maximum…
Let $p',q'\in R^n$. Write $p'\sim q'$ if $p'-q'$ is a multiple of $(1,\ldots,1)$. Two different points $p$ and $q$ in $R^n/\sim$ uniquely determine a tropical line $L(p,q)$, passing through them, and stable under small perturbations. This…
A long-standing conjecture on spanning trees of a hypercube states that a balanced tree on $2^n$ vertices with maximum degree at most $3$ spans the hypercube of dimension $n$ \cite{havel1986}. In this paper, we settle the conjecture for a…
A Yule tree is the result of a branching process with constant birth and death rates. Such a process serves as an instructive null model of many empirical systems, for instance, the evolution of species leading to a phylogenetic tree.…
This article concerns the following question arising in computational evolutionary biology. For a given subclass of phylogenetic networks, what is the maximum value of 0 <= p <= 1 such that for every input set T of rooted triplets, there…
A subset of vertices is a {\it maximum independent set} if no two of the vertices are adjacent and the subset has maximum cardinality. A subset of vertices is called a {\it maximum dissociation set} if it induces a subgraph with vertex…