Related papers: On the maximum quartet distance between phylogenet…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
We show that the maximum number of unit distances or of diameters in a set of n points in d-dimensional Euclidean space is attained only by specific types of Lenz constructions, for all d >= 4 and n sufficiently large, depending on d. As a…
The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the…
In phylogenetic networks, it is desirable to estimate edge lengths in substitutions per site or calendar time. Yet, there is a lack of scalable methods that provide such estimates. Here we consider the problem of obtaining edge length…
We present two algorithms for computing the geodesic distance between phylogenetic trees in tree space, as introduced by Billera, Holmes, and Vogtmann (2001). We show that the possible combinatorial types of shortest paths between two trees…
Loebl, Komlos, and Sos conjectured that if at least half the vertices of a graph G have degree at least some k, then every tree with at most k edges is a subgraph of G. We prove the conjecture for all trees of diameter at most 5 and for a…
The subtrees and BC-subtrees (subtrees where any two leaves are at even distance apart) have been extensively studied in recent years. Such structures, under special constraints on degrees, have applications in many fields. Through an…
The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…
The size of the largest common subtree (maximum agreement subtree) of two independent uniform random binary trees on $n$ leaves is known to be between orders $n^{1/8}$ and $n^{1/2}$. By a construction based on recursive splitting and…
We give a counterexample to the conjecture of Martin and Thatte that two balanced rooted binary leaf-labelled trees on $n$ leaves have a maximum agreement subtree (MAST) of size at least $n^{\frac{1}{2}}$. In particular, we show that for…
The rooted subtree prune and regraft (rSPR) distance between two rooted binary phylogenetic trees is a well-studied measure of topological dissimilarity that is NP-hard to compute. Here we describe an improved linear kernel for the problem.…
The rank (also known as protection number or leaf-height) of a vertex in a rooted tree is the minimum distance between the vertex and any of its leaf descendants. We consider the sum of ranks over all vertices (known as the security) in…
The problems of maximizing the spectral radius and the number of spanning trees in a class of bipartite graphs with certain degree constraints are considered. In both the problems, the optimal graph is conjectured to be a Ferrers graph.…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…
It is known that graphs on n vertices with minimum degree at least 3 have spanning trees with at least n/4+2 leaves and that this can be improved to (n+4)/3 for cubic graphs without the diamond K_4-e as a subgraph. We generalize the second…
Quartet Reconstruction, the task of recovering a phylogenetic tree from smaller trees on four species called \textit{quartets}, is a well-studied problem in theoretical computer science with far-reaching connections to statistics, graph…
In Francis and Steel (2015), it was shown that there exists non-trivial networks on $4$ leaves upon which the distance metric affords a metric on a tree which is not the base tree of the network. In this paper we extend this result in two…
Let $M$ be a simple 3-manifold such that one component of $\partial M$, say $F$, has genus at least two. For a slope $\alpha$ on $F$, we denote by $M(\alpha)$ the manifold obtained by attaching a 2-handle to $M$ along a regular neighborhood…
A conjecture of Luo, Tian and Wu (2022) says that for every positive integer $k$ and every finite tree $T$ with bipartition $X$ and $Y$ (denote $t = \max\{|X|,|Y |\})$, every $k$-connected bipartite graph $G$ with $\delta(G) \geq k + t$…
Distance based algorithms are a common technique in the construction of phylogenetic trees from taxonomic sequence data. The first step in the implementation of these algorithms is the calculation of a pairwise distance matrix to give a…