Related papers: Reconstructing fully-resolved trees from triplet c…
Binets and trinets are phylogenetic networks with two and three leaves, respectively. Here we consider the problem of deciding if there exists a binary level-1 phylogenetic network displaying a given set $\mathcal{T}$ of binary binets or…
Given a tree $T$ on $n$ vertices, and $k, b, s_1, \ldots, s_b \in N$, the Tree Partitioning problem asks if at most $k$ edges can be removed from $T$ so that the resulting components can be grouped into $b$ groups such that the number of…
Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…
Developing a robust algorithm for automatic individual tree crown (ITC) detection from laser scanning datasets is important for tracking the responses of trees to anthropogenic change. Such approaches allow the size, growth and mortality of…
Weighted recursive trees are built by adding successively vertices with predetermined weights to a tree: each new vertex is attached to a parent chosen randomly proportionally to its weight. Under some assumptions on the sequence of…
A {\it tiered graph} $G=(V,E)$ with $m $ tiers is a simple graph with $V\subseteq \brk{n}$, where $\brk{n}=\{1,2,\cdots,n\}$, and with a surjective map $t$ from $V$ to $\brk{m}$ such that if $v$ is a vertex adjacent to $v'$ in $G$ with…
This paper proves the reconstruction conjecture for graphs which are isomorphic to the cube of a tree. The proof uses the reconstructibility of trees from their peripheral vertex deleted subgraphs. The main result follows from (i)…
In this paper and a companion paper, we prove that, if $m$ is sufficiently large, every graph on $m+1$ vertices that has a universal vertex and minimum degree at least $\lfloor \frac{2m}{3} \rfloor$ contains each tree $T$ with $m$ edges as…
For a tree $T$, let $lp(T)$ be the number of different lengths of leaf to leaf paths in $T$. For a degree sequence $s$ of a tree, let ${\rm rad}(s)$ be the minimum radius of a tree with degree sequence $s$. Recently, Di Braccio,…
In this article, we propose tree edit distance with variables, which is an extension of the tree edit distance to handle trees with variables and has a potential application to measuring the similarity between mathematical formulas,…
We study the natural problem of Triplet Reconstruction (also Rooted Triplets Consistency or Triplet Clustering), originally motivated in computational biology and relational databases (Aho, Sagiv, Szymanski, and Ullman, 1981): given $n$…
Network topology plays a key role in many phenomena, from the spreading of diseases to that of financial crises. Whenever the whole structure of a network is unknown, one must resort to reconstruction methods that identify the least biased…
Assume that we embed the path $P_n$ as a subgraph of a $2$-dimensional grid, namely, $P_k \times P_l$. Given such an embedding, we consider the ordered set of subpaths $L_1, L_2, \ldots , L_m$ which are maximal straight segments in the…
We characterize the extremal trees that maximize the number of almost-perfect matchings, which are matchings covering all but one or two vertices, and those that maximize the number of strong almost-perfect matchings, which are matchings…
The widely studied edge modification problems ask how to minimally alter a graph to satisfy certain structural properties. In this paper, we introduce and study a new edge modification problem centered around transforming a given graph into…
One of the goals of phylogenetic research is to find the species tree describing the evolutionary history of a set of species. But the trees derived from geneti data with the help of tree inference methods are gene trees that need not…
Given natural limitations on the length DNA sequences, designing phylogenetic reconstruction methods which are reliable under limited information is a crucial endeavor. There have been two approaches to this problem: reconstructing partial…
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…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…
Tree-width has been proven to be a useful parameter to design fast and efficient algorithms for intractable problems. However, while tree-width is low on relatively sparse graphs can be arbitrary high on dense graphs. Therefore, we…