Related papers: Minimum triplet covers of binary phylogenetic $X$-…
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…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
We prove that finding a rooted subtree with at least $k$ leaves in a digraph is a fixed parameter tractable problem. A similar result holds for finding rooted spanning trees with many leaves in digraphs from a wide family $\cal L$ that…
Let $T$ be a tree with $t$ edges. We show that the number of isomorphic (labeled) copies of $T$ in a graph $G = (V,E)$ of minimum degree at least $t$ is at least \[2|E| \prod_{v \in V} (d(v) - t + 1)^{\frac{(t-1)d(v)}{2|E|}}.\]…
It follows from a classical result of Jordan that every tree with maximum degree at most $r$ containing a vertex set labeled by $[n]$, has a single-edge cut which separates two subsets $A,B \subset [n]$ for which $\min\{|A|,|B|\} \ge…
Minimal spanning trees on infinite vertex sets are investigated. A criterion for minimality of a spanning tree having a finite length is obtained, which generalizes the corresponding classical result for finite sets. It is given an analytic…
It was recently shown that a large class of phylogenetic networks, the `labellable' networks, is in bijection with the set of `expanding' covers of finite sets. In this paper, we show how several prominent classes of phylogenetic networks…
The leafage of a digraph is the minimum number of leaves in a host tree in which it has a subtree intersection representation. We discuss bounds on the leafage in terms of other parameters (including Ferrers dimension), obtaining a string…
Given two binary trees on $N$ labeled leaves, the quartet distance between the trees is the number of disagreeing quartets. By permuting the leaves at random, the expected quartets distance between the two trees is…
This paper introduces a new combinatorial framework for modeling the growth of binary trees through a discrete evolution process that incorporates a growing rule and an extinction rule. Building upon the theory of increasingly labeled…
Let $T$ be a tree, a vertex of degree one is a leaf of $T$ and a vertex of degree at least three is a branch vertex of $T$. For two distinct vertices $u,v$ of $T$, let $P_T[u,v]$ denote the unique path in $T$ connecting $u$ and $v.$ For a…
Given a tree $T$, its 3-coloring graph $\mathcal{C}_3(T)$ has as vertices the proper 3-colorings of $T$, with edges joining colorings that differ at exactly one vertex. We call the diameter of $\mathcal{C}_3(T)$ the 3-coloring diameter of…
We investigate the structure of trees that have minimal algebraic connectivity among all trees with a given degree sequence. We show that such trees are caterpillars and that the vertex degrees are non-decreasing on every path on…
In a rooted tree, we call a vertex {\em balanced} if it is at equal distance from all its descendant leaves. We count balanced vertices in three different tree varieties. For decreasing binary trees, we can prove that the probability that a…
Phylogenetic networks are a generalization of evolutionary trees that are used by biologists to represent the evolution of organisms which have undergone reticulate evolution. Essentially, a phylogenetic network is a directed acyclic graph…
Rooted triples, rooted binary phylogenetic trees on three leaves, are sufficient to encode rooted binary phylogenetic trees. That is, if $\mathcal T$ and $\mathcal T'$ are rooted binary phylogenetic $X$-trees that infers the same set of…
The atom-bond connectivity (ABC) index is a degree-based molecular descriptor with diverse chemical applications. Recent work of Lin et al. [W. Lin, J. Chen, C. Ma, Y. Zhang, J. Chen, D. Zhang, and F. Jia, On trees with minimal ABC index…
We study minimal vertex covers of trees. Contrarily to the number $N_{vc}(A)$ of minimal vertex covers of the tree $A$, $\log N_{vc}(A)$ is a self-averaging quantity. We show that, for large sizes $n$, $\lim_{n\to +\infty} <\log…
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…
Unrooted phylogenetic networks are graphs used to represent evolutionary relationships. Accurately reconstructing such networks is of great relevance for evolutionary biology. It has recently been conjectured that all phylogenetic networks…