Related papers: Toric ideals of homogeneous phylogenetic models
Group-based models appear in algebraic statistics as mathematical models coming from evolutionary biology, respectively the study of mutations of organisms. Both theoretically and in terms of applications, we are interested in determining…
The strand symmetric model is a phylogenetic model designed to reflect the symmetry inherent in the double-stranded structure of DNA. We show that the set of known phylogenetic invariants for the general strand symmetric model of the three…
We consider absolutely free nonassociative algebras and, more generally, absolutely free algebras with (maybe infinitely) many multilinear operations. Such algebras are described in terms of labeled reduced planar rooted trees. This allows…
We study an inductive method of computing initial ideals and Gr\"obner bases for families of ideals in a polynomial ring. This method starts from a given set of pairs $(I,J)$ where $I$ is any ideal and $J$ is a monomial ideal contained in…
Let $G$ be a finite graph allowing loops, having no multiple edge and no isolated vertex. We associate $G$ with the edge polytope ${\cal P}_G$ and the toric ideal $I_G$. By classifying graphs whose edge polytope is simple, it is proved that…
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…
Given any equigenerated monomial ideal $I$ with the property that the defining ideal $J$ of the fiber cone $ F(I)$ of $I$ is generated by quadratic binomials, we introduce a matrix such that the set of its binomial $2$-minors is a…
The mathematical modelling of genetic-metabolic networks is of out most importance in the field of systems biology. Different formalisms and a huge variety of classical mathematical tools have been used to describe and analyse such…
Bounds for the maximum degree of a minimal Gr\"obner basis of simplicial toric ideals with respect to the reverse lexicographic order are given. These bounds are close to the bound stated in Eisenbud-Goto's Conjecture on the…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
We consider extremal problems related to decks and multidecks of rooted binary trees (a.k.a. rooted phylogenetic tree shapes). Here, the deck (resp. multideck) of a tree $T$ refers to the set (resp. multiset) of leaf induced binary subtrees…
A \textit{symmetric ideal} $I \subseteq R = K[x_1,x_2,...]$ is an ideal that is invariant under the natural action of the infinite symmetric group. We give an explicit algorithm to find Gr\"obner bases for symmetric ideals in the infinite…
In the present paper, we prove that the toric ideals of certain $s$-block diagonal matching fields have quadratic Gr\"obner bases. Thus, in particular, those are quadratically generated. By using this result, we provide a new family of…
We introduce an efficient way, called Newton algorithm, to study arbitrary ideals in C[[x,y]], using a finite succession of Newton polygons. We codify most of the data of the algorithm in a useful combinatorial object, the Newton tree. For…
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.…
Recently, it was shown that a binary linear code can be associated to a binomial ideal given as the sum of a toric ideal and a non-prime ideal. Since then two different generalizations have been provided which coincide for the binary case.…
Given a rooted tree $T$ on $n$ non-root leaves with colored and zeroed nodes, we construct a linear space $L_T$ of $n\times n$ symmetric matrices with constraints determined by the combinatorics of the tree. When $L_T$ represents the…
We study the algebraic combinatorics of monomial degenerations of Pl\"ucker forms which is governed by matching fields in the sense of Sturmfels and Zelevinsky. We provide a necessary condition for a matching field to yield a Khovanskii…
We introduce some natural families of distributions on rooted binary ranked plane trees with a view toward unifying ideas from various fields, including macroevolution, epidemiology, computational group theory, search algorithms and other…
We introduce polytopal cell complexes associated with partial acyclic orientations of a simple graph, which generalize acyclic orientations. Using the theory of cellular resolutions, two of these polytopal cell complexes are observed to…