Related papers: Phylogenetic degrees for Jukes-Cantor model
Toric quiver varieties (moduli spaces of quiver representations) are studied. Given a quiver and a weight there is an associated quasiprojective toric variety together with a canonical embedding into projective space. It is shown that for a…
Here we introduce researchers in algebraic biology to the exciting new field of cophylogenetics. Cophylogenetics is the study of concomitantly evolving organisms (or genes), such as host and parasite species. Thus the natural objects of…
Phylogenetic inference, grounded in molecular evolution models, is essential for understanding the evolutionary relationships in biological data. Accounting for the uncertainty of phylogenetic tree variables, which include tree topologies…
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…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
A phylogenetic tree is an important way in Bioinformatics to find the evolutionary relationship among biological species. In this research, a proposed model is described for the estimation of a phylogenetic tree for a given set of data. To…
We show that the height of a toric variety with respect to a toric metrized line bundle can be expressed as the integral over a polytope of a certain adelic family of concave functions. To state and prove this result, we study the Arakelov…
Phylogenetics is the study of the evolutionary relationships between organisms. One of the main challenges in the field is to take biological data for a group of organisms and to infer an evolutionary tree, a graph that represents these…
Given a group-based Markov model on a tree, one can compute the vertex representation of a polytope which describes the associated toric variety. The half-space representation, however, is not easily computable. In the case of…
A phylogenetic birth-and-death model is a probabilistic graphical model for a so-called phylogenetic profile, i.e., the size distribution for a homolog gene family at the terminal nodes of a phylogeny. Profile datasets are used in…
We define the tropical Tevelev degrees, $\mathsf{Tev}_g^{trop}$, as the degree of a natural finite morphism between certain tropical moduli spaces, in analogy to the algebraic case. We develop an explicit combinatorial construction that…
We study tropical degree bounds, stable tropical intersections, and tropical B\'ezout-type estimates through the geometry of Newton polytopes, mixed subdivisions, and lattice indices. We establish an upper bound for the tropical degree of a…
A calculational framework is proposed for phylogenetics, using nonlocal quantum field theories in hypercubic geometry. Quadratic terms in the Hamiltonian give the underlying Markov dynamics, while higher degree terms represent branching…
We study the combinatorial geometry of "lattice" Jenkins--Strebel differentials with simple zeroes and simple poles on $\mathbb{C}P^1$ and of the corresponding counting functions. Developing the results of M. Kontsevich we evaluate the…
We find a relation between mixed volumes of several polytopes and the convex hull of their union, deducing it from the following fact: the mixed volume of a collection of polytopes only depends on the product of their support functions…
Identifiability of phylogenetic models is a necessary condition to ensure that the model parameters can be uniquely determined from data. Mixture models are phylogenetic models where the probability distributions in the model are convex…
We consider the phylogenetic tree model in which every node of the tree is observed and binary and the transitions are given by the same matrix on each edge of the tree. We are able to compute the Grobner basis and Markov basis of the toric…
A general problem in complex cobordism theory is to find useful representatives for cobordism classes. One particularly convenient class of complex manifolds consists of smooth projective toric varieties. The bijective correspondence…
For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…
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…