Related papers: Phylogenetic invariants for group-based models
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
A theory of finite type invariants for arbitrary compact oriented 3-manifolds is proposed, and illustrated through many examples arising from both classical and quantum topology. The theory is seen to be highly non-trivial even for…
A simple method of constructing a big stock of algebraic varieties with trivial Makar-Limanov invariant is described, the Derksen invariant of some varieties is computed, the generalizations of the Makar-Limanov and Derksen invariants are…
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…
The goal of invariant theory is to find all the generators for the algebra of representations of a group that leave the group invariant. Such generators will be called \emph{basic invariants}. In particular, we set out to find the set of…
This work is dedicated to the consideration of the construction of a representation of braid group generators from vertex models with $N$-states, which provides a great way to study the knot invariant. An algebraic formula is proposed for…
In this paper we complete the results of Sullivant and Sturmfels proving that many of the algebraic group-based models for Markov processes on trees are pseudo-toric. We also show in which cases these varieties are normal. This is done by…
We prove that the phylogenetic complexity -- an invariant introduced by Sturmfels and Sullivant -- of any finite abelian group is finite.
A cluster algebra is a commutative algebra whose structure is decided by a skew-symmetrizable matrix or a quiver. When a skew-symmetrizable matrix is invariant under an action of a finite group and this action is admissible, the folded…
We partially generalize the theory of semihomogeneous bundles on an abelian variety $A$ developed by Mukai. This involves considering abelian subvarieties $Y\subset X_A=A\times\hat{A}$ and studying coherent sheaves on $A$ invariant under…
We study the Gorenstein property for phylogenetic group-based models. We prove that for the groups $\mathbb Z_3$ and $\mathbb Z_2\times \mathbb Z_2$ and trivalent trees the associated polytopes are always Gorenstein extending the results of…
Let $U/K$ be a smooth affine curve over a number field and let $L$ be an irreducible rank 3 $\overline{\mathbb Q}_{\ell}$-local system on $U$ with trivial determinant and infinite geometric monodromy around a cusp. Suppose further that $L$…
We find presentations for subalgebras of invariants of the coordinate algebras of binary symmetric models of phylogenetic trees studied by Buczynska and Wisniewski in \cite{BW}. These algebras arise as toric degenerations of rings of global…
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 a previous paper, we showed that all the cohomological invariants of Weyl groups are completely determined by their restrictions to the abelian subgroups generated by reflections. Using this principle, we describe all the cohomological…
Let $A$ be an abelian variety over a global function field $K$ of characteristic $p$. We study the $\mu$-invariant appearing in the Iwasawa theory of $A$ over the unramified $\mathbb{Z}_p$-extension of $K$. Ulmer suggests that this…
We introduce a new family of invariants of real algebraic sets defined in terms of the topology of their complexifications and compute some of these invariants for spheres. This allows us to completely classify topological isomorphism…
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…
The variety of bicommutative algebras consists of all nonassociative algebras satisfying the polynomial identities of right- and left-commutativity $(x_1x_2)x_3=(x_1x_3)x_2$ and $x_1(x_2x_3)=x_2(x_1x_3)$. Let $F_d$ be the free $d$-generated…
We study the enumerative geometry of algebraic curves on abelian surfaces and threefolds. In the abelian surface case, the theory is parallel to the well-developed study of the reduced Gromov-Witten theory of K3 surfaces. We prove complete…