Related papers: The disentangling number for phylogenetic mixtures
Phylogenetic mixture models are statistical models of character evolution allowing for heterogeneity. Each of the classes in some unknown partition of the characters may evolve by different processes, or even along different trees. The…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
We determine upper and lower bounds for the number of maximum matchings (i.e., matchings of maximum cardinality) $m(T)$ of a tree $T$ of given order. While the trees that attain the lower bound are easily characterised, the trees with…
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…
We prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different…
We study the joint distribution of the number of occurrences of members of a collection of nonoverlapping motifs in digital data. We deal with finite and countably infinite collections. For infinite collections, the setting requires that we…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
We investigate the rank of the average mixing matrix of trees, with all eigenvalues distinct. The rank of the average mixing matrix of a tree on $n$ vertices with $n$ distinct eigenvalues is upper-bounded by $\frac{n}{2}$. Computations on…
Motivated by the properties of the descent polynomials, which enumerate permutations of $S_n$ with a fixed descent set, we define descent polynomials for labeled rooted trees. We give recursive and explicit formulas for these polynomials…
In this paper we apply new geometric and combinatorial methods to the study of phylogenetic mixtures. The focus of the geometric approach is to describe the geometry of phylogenetic mixture distributions for the two state random cluster…
In 1989 Erd\H{o}s and Sz\'ekely showed that there is a bijection between (i) the set of rooted trees with $n+1$ vertices whose leaves are bijectively labeled with the elements of $[\ell]=\{1,2,\dots,\ell\}$ for some $\ell \leq n$, and (ii)…
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…
We obtain sharp lower and upper bounds for the number of maximal (under inclusion) independent sets in trees with fixed number of vertices and diameter. All extremal trees are described up to isomorphism.
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
We show that there exists a family of instances of the lot-sizing problem, such that any branch-and-bound tree that solves them requires an exponential number of nodes, even in the case when the branchings are performed on general split…
Rooted binary perfect phylogenies provide a generalization of rooted binary unlabeled trees in which each leaf is assigned a positive integer value that corresponds in a biological setting to the count of the number of indistinguishable…
A tanglegram is a pair of binary trees with the same set of leaves. Unlabeled tanglegrams were counted recently by Billey, Konvalinka, and Matsen, who also proposed the problem of counting several variations of unlabeled tanglegrams…
Labeled unranked trees are used as a model of XML documents, and logical languages for them have been studied actively over the past several years. Such logics have different purposes: some are better suited for extracting data, some for…