Related papers: Phylogenetic toric varieties on graphs

Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…

Firstly, for a general graph, we find a recursion formula on the number of Hamiltonian cycles and one on cycles. By this result, we give some new polynomial invariants. Secondly, we give a condition to tell whether a polynomial defined by…

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…

The Cox ring provides a coordinate system on a toric variety analogous to the homogeneous coordinate ring of projective space. Rational maps between projective spaces are described using polynomials in the coordinate ring, and we generalise…

Recent years have seen a rapid expansion of the model space explored in statistical phylogenetics, emphasizing the need for new approaches to statistical model representation and software development. Clear communication and representation…

The toric Hilbert scheme is a parameter space for all ideals with the same multi-graded Hilbert function as a given toric ideal. Unlike the classical Hilbert scheme, it is unknown whether toric Hilbert schemes are connected. We construct a…

We consider several algebras that arise in the study of the mapping class group (by means of topology and Hodge theory) and describe their symplectic-invariant parts in terms of algebras on trivalent graphs.

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…

We introduce new methods for phylogenetic tree quartet construction by using machine learning to optimize the power of phylogenetic invariants. Phylogenetic invariants are polynomials in the joint probabilities which vanish under a model of…

We define scrollar invariants of tropical curves with a fixed divisor of rank 1. We examine the behavior of scrollar invariants under specialization, and provide an algorithm for computing these invariants for a much-studied family of…

In this paper we illustrate an algorithmic procedure which allows to build projective wonderful models for the complement of a toric arrangement in a n-dimensional algebraic torus T. The main step of the construction is a combinatorial…

We show that the isolated invariant branches globalize to algebraic curves, when we consider weak toric type complex hyperbolic foliations on projective toric ambient surfaces. To do it, we pass through a characterization of weak toric type…

We will consider P-graph complexes, where P is a cyclic operad. P-graph complexes are natural generalizations of Kontsevich's graph complexes -- for P = the operad for associative algebras it is the complex of ribbon graphs, for P = the…

Generalizing cones over projective toric varieties, we present arbitrary toric varieties as quotients of quasiaffine toric varieties. Such quotient presentations correspond to groups of Weil divisors generating the topology. Groups…

We apply classical invariant theory of binary forms to explicitly characterize isomorphism classes of hyperelliptic curves of small genus and, conversely, propose algorithms for reconstructing hyperelliptic models from given invariants. We…

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.…

Evolution algebras are a special class of non-associative algebras exhibiting connections with different fields of Mathematics. Hilbert evolution algebras generalize the concept through a framework of Hilbert spaces. This allows to deal…

We introduce tropical complexes, as an enrichment of the dual complex of a degeneration with additional data from non-transverse intersection numbers. We define cycles, divisors, and linear equivalence on tropical complexes, analogous both…

Given a toric degeneration (a degeneration to a toric variety), over the complex numbers, we construct a surjective continuous map from a general fiber to the special fiber of the degeneration in the classical topology. The construction is…

A rooted phylogenetic network is a directed acyclic graph with a single root, whose sinks correspond to a set of species. As such networks are useful for representing the evolution of species that have undergone reticulate evolution, there…