Related papers: Phylogenetic degrees for Jukes-Cantor model
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
A family of polynomials parameterized by the conjugacy classes of a finite Coxeter group is investigated. These polynomials, together with the character table of the group, determine the associated generic degrees. The polynomials are…
A polytrope is a tropical polyhedron that is also classically convex. We study the tropical combinatorial types of polytropes associated to weighted directed acyclic graphs (DAGs). This family of polytropes arises in algebraic statistics…
On tropical geometry in $\rr^2$, the divisor and the Jacobian variety are defined in analogy to algebraic geometry. For study of these objects, it is important to think of the `bunch' of a tropical curve. In this paper, we will show that if…
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…
The purpose of this note is to give an exposition of some interesting combinatorics and convex geometry concepts that appear in algebraic geometry in relation to counting the number of solutions of a system of polynomial equations in…
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 introduce tropical analogues of the notion of volume of polytopes, leading to a tropical version of the (discrete) classical isoperimetric inequality. The planar case is elementary, but a higher-dimensional generalization leads to an…
Phylogenetic networks are a generalization of evolutionary or phylogenetic trees that are commonly used to represent the evolution of species which cross with one another. A special type of phylogenetic network is an {\em $X$-cactus}, which…
Classification of gene trees is an important task both in the analysis of multi-locus phylogenetic data, and assessment of the convergence of Markov Chain Monte Carlo (MCMC) analyses used in Bayesian phylogenetic tree reconstruction. The…
We introduce a collection of convex polytopes associated to a torus-equivariant vector bundle on a smooth complete toric variety. We show that the lattice points in these polytopes correspond to generators for the space of global sections…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
The phylogenetic semigroup on a graph generalizes the Jukes-Cantor binary model on a tree. Minimal generating sets of phylogenetic semigroups have been described for trivalent trees by Buczy\'nska and Wi\'sniewski, and for trivalent graphs…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
A staged tree model is a discrete statistical model encoding relationships between events. These models are realised by directed trees with coloured vertices. In algebro-geometric terms, the model consists of points inside a toric variety.…
Distance-based methods such as UPGMA (Unweighted Pair Group Method with Arithmetic Mean) continue to play a significant role in phylogenetic research. We use polyhedral combinatorics to analyze the natural subdivision of the positive…
Comparing and computing distances between phylogenetic trees are important biological problems, especially for models where edge lengths play an important role. The geodesic distance measure between two phylogenetic trees with edge lengths…
The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies…
Phylogenetic networks provide a means of describing the evolutionary history of sets of species believed to have undergone hybridization or gene flow during their evolution. The mutation process for a set of such species can be modeled as a…
Felsenstein's classical model for Gaussian distributions on a phylogenetic tree is shown to be a toric variety in the space of concentration matrices. We present an exact semialgebraic characterization of this model, and we demonstrate how…