Related papers: Polyhedral Covers of Tree Space
The tree complex is a simplicial complex defined in recent work of Belk, Lanier, Margalit, and Winarski with natural applications to mapping class groups and complex dynamics. In this article, we connect this setting with the study of…
A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube…
The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…
An associahedron is a polytope whose vertices correspond to triangulations of a convex polygon and whose edges correspond to flips between them. Using labeled polygons, C. Hohlweg and C. Lange constructed various realizations of the…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
The phylogenetic tree space introduced by Billera, Holmes, and Vogtmann (BHV tree space) is a CAT(0) continuous space that represents trees with edge weights with an intrinsic geodesic distance measure. The geodesic distance measure unique…
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…
Phylogenetic trees provide a fundamental representation of evolutionary relationships, yet the combinatorial explosion of possible tree topologies renders inference computationally challenging. Classical approaches to characterizing tree…
Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…
The polytope structure of the associahedron is decomposed into two categories, types and classes. The classification of types is related to integer partitions, whereas the classes present a new combinatorial problem. We solve this and…
We prove a conjecture of Bahri, Bendersky, Cohen and Gitler: if K is a shifted simplicial complex on n vertices, X_1,..., X_n are spaces and CX_i is the cone on X_i, then the polyhedral product determined by K and the pairs (CX_i,X_i) is…
Monotone path polytopes arise as a special case of the construction of fiber polytopes, introduced by Billera and Sturmfels. A simple example is provided by the permutahedron, which is a monotone path polytope of the standard unit cube. The…
Given a tree $T$, its path polytope is the convex hull of the edge indicator vectors for the paths between any two distinct leaves in $T$. These polytopes arise naturally in polyhedral geometry and applications, such as phylogenetics,…
The multiplihedra {M_n} form a family of polytopes originating in the study of higher categories and homotopy theory. While the multiplihedra may be unfamiliar to the algebraic combinatorics community, it is nestled between two families of…
An associahedron is a polytope whose vertices correspond to the triangulations of a convex polygon and whose edges correspond to flips between them. A particularly elegant realization of the associahedron, due to S. Shnider and S. Sternberg…
A polyhedral product is a natural subspace of a Cartesian product that is specified by a simplicial complex. The modern formalism arose as a generalization of the spaces known as moment-angle complexes which were developed within the…
A phylogenetic tree is an edge-weighted binary tree, with leaves labelled by a collection of species, that represents the evolutionary relationships between those species. For such a tree, a phylogenetic diversity index is a function that…
In tropical algebraic geometry, the solution sets of polynomial equations are piecewise-linear. We introduce the tropical variety of a polynomial ideal, and we identify it with a polyhedral subcomplex of the Grobner fan. The tropical…
We study the behavior of phylogenetic tree shapes in the tropical geometric interpretation of tree space. Tree shapes are formally referred to as tree topologies; a tree topology can also be thought of as a tree combinatorial type, which is…
Combinatorial Hopf algebras of trees exemplify the connections between operads and bialgebras. Painted trees were introduced recently as examples of how graded Hopf operads can bequeath Hopf structures upon compositions of coalgebras. We…