Related papers: On the maximum quartet distance between phylogenet…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Let $G$ be a finite, connected graph and $v$ a vertex of $G$. The average distance and the eccentricity of $v$ in $G$ are defined as the arithmetic mean and the maximum, respectively, of the distances from $v$ to all other vertices of $G$.…
In many interesting cases the reconstruction of a correct phylogeny is blurred by high mutation rates and/or horizontal transfer events. As a consequence a divergence arises between the true evolutionary distances and the differences…
The Wiener index of a connected graph is the sum of topological distances between all pairs of vertices. Since Wang gave a mistake result on the maximum Wiener index for given tree degree sequence, in this paper, we investigate the maximum…
The Wiener index of a connected graph is defined as the sum of distances between all its unordered pairs of vertices. Characterising graphs on $n$ vertices with a fixed diameter that maximise the Wiener index is a long-standing open…
Phylogenetic reconciliation seeks to explain host-symbiont co-evolution by mapping parasite trees onto host trees through events such as cospeciation, duplication, host switching, and loss. Finding an optimal reconciliation that ensures…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we improve known parameterized algorithms and…
Maximum distance profile codes are characterized by the property that two trajectories which start at the same state and proceed to a different state will have the maximum possible distance from each other relative to any other…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
In 1959, Erd\H{o}s and Moser asked for the maximum number of unit distances that may be formed among the vertices of a convex $n$-gon; until now, the best known upper bound has been $2\pi n \log_2 n + O(n)$, achieved by F\"uredi in 1990. In…
Phylogenetic networks generalize phylogenetic trees by allowing reticulate evolutionary events such as horizontal gene transfer and hybridization. Among the many subclasses of phylogenetic networks, orchard networks have attracted…
The Maximum Agreement Forest (Maf) problem is a well-studied problem in evolutionary biology, which asks for a largest common subforest of a given collection of phylogenetic trees with identical leaf label-set. However, the previous work…
Rotation distance between trees measures the number of simple operations it takes to transform one tree into another. There are no known polynomial-time algorithms for computing rotation distance. In the case of ordered rooted trees, we…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
We call a pair of vertex-disjoint, induced subtrees of a rooted trees twins if they have the same counts of vertices by out-degrees. The likely maximum size of twins in a uniformly random, rooted Cayley tree of size $n\to\infty$ is studied.…
For a tree with the given sequence of vertex degrees the spectral radius of its terminal distance matrix is shown to be bounded from below by the the average row sum of the terminal distance matrix of the, so called, BFS-tree (also known as…
Measures of tree balance play an important role in different research areas such as mathematical phylogenetics or theoretical computer science. The balance of a tree is usually quantified in a single number, called a balance or imbalance…
Over some types of trees with a given number of vertices, which trees minimize or maximize the total number of subtrees or leaf containing subtrees are studied. Here are some of the main results:\ (1)\, Sharp upper bound on the total number…
In this paper we introduce and study three new measures for efficient discriminative comparison of phylogenetic trees. The NNI navigation dissimilarity $d_{nav}$ counts the steps along a "combing" of the Nearest Neighbor Interchange (NNI)…
The {\sc Directed Maximum Leaf Out-Branching} problem is to find an out-branching (i.e. a rooted oriented spanning tree) in a given digraph with the maximum number of leaves. In this paper, we obtain two combinatorial results on the number…