相关论文: Toric ideals of homogeneous phylogenetic models
The properties of randomly evolving special trees having defined and analyzed already in two earlier papers (arXiv:cond-mat/0205650 and arXiv:cond-mat/0211092) have been investigated in the case when the continuous time parameter converges…
The probability that two randomly selected phylogenetic trees of the same size are isomorphic is found to be asymptotic to a decreasing exponential modulated by a polynomial factor. The number of symmetrical nodes in a random phylogenetic…
Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…
Let $n \ge 2$ be an integer. In this note, we show that the {\it oriented} transition matrices over the field $\mathcal R$ of all real numbers (over the finite field $\mathcal Z_2$ of two elements respectively) of all continuous {\it vertex…
It is known that all but finitely many leaves of a measured foliated 2-complex of thin type are quasi-isometric to an infinite tree with at most two topological ends. We show that if the foliation is cooriented, and the associated R-tree is…
In this paper, the concepts of binomial difference ideals and toric difference varieties are defined and their properties are proved. Two canonical representations for Laurent binomial difference ideals are given using the reduced Groebner…
Let $I = ( f_1, \dots, f_n )$ be a homogeneous ideal in the polynomial ring $K[x_1, \dots,x_n]$ over a field $K$ generated by generic polynomials. Using an incremental approach based on a method by Gao, Guan and Volny, and properties of the…
A universal Gr\"obner basis of an ideal is the union of all its reduced Gr\"obner bases. It is contained in the Graver basis, the set of all primitive elements. Obtaining an explicit description of either of these sets, or even a sharp…
Tropical ideals, introduced in arXiv:1609.03838, define subschemes of tropical toric varieties. We prove that the top-dimensional parts of their varieties are balanced polyhedral complexes of the same dimension as the ideal. This means that…
Phylogenetic networks generalize phylogenetic trees by allowing the modelization of events of reticulate evolution. Among the different kinds of phylogenetic networks that have been proposed in the literature, the subclass of binary…
A numerical semigroup is said to be universally free if it is free for any possible arrangement of its minimal generating set. In this work, we establish that toric ideals associated with universally free numerical semigroups can be…
We carry out a complete analysis of the toric elliptic and genus-one fibrations of all 474 million reflexive polytopes in the Kreuzer-Skarke database. Earlier work with Huang showed that all but 29,223 of these polytopes have such a…
We provide an $\Omega(n\log n) $ lower bound and an $O(n^2)$ upper bound for the smallest size of rooted binary trees (a.k.a. phylogenetic tree shapes), which are universal for rooted binary trees with $n$ leaves, i.e., contain all of them…
By introducing the notions of living and dead nodes a new model of random tree evolution with continuous time parameter has been constructed. It is assumed that two random variables, the lifetime and the offspring number of living nodes…
We introduce and study a special class of ideals, called tropical ideals, in the semiring of tropical polynomials, with the goal of developing a useful and solid algebraic foundation for tropical geometry. The class of tropical ideals…
Methods of phylogenetic inference use more and more complex models to generate trees from data. However, even simple models and their implications are not fully understood. Here, we investigate the two-state Markov model on a tripod tree,…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…
It has been conjectured that the toric ideal of the base ring of a discrete polymatroid is generated by symmetric exchange binomials. In the present paper, we give several classes of discrete polymatroids which yield toric ideals generated…
The Rabin tree theorem yields an algorithm to solve the satisfiability problem for monadic second-order logic over infinite trees. Here we solve the probabilistic variant of this problem. Namely, we show how to compute the probability that…
Monadic second order logic can be used to express many classical notions of sets of vertices of a graph as for instance: dominating sets, induced matchings, perfect codes, independent sets or irredundant sets. Bounds on the number of sets…