Related papers: Phylogenetic invariants for $\mathbb{Z}_3$ scheme-…
In this paper we investigate properties of algebraic varieties representing group-based phylogenetic models. We propose a method of generating many phylogenetic invariants. We prove that we obtain all invariants for any tree for the binary…
We study phylogenetic complexity of finite abelian groups - an invariant introduced by Sturmfels and Sullivant. The invariant is hard to compute - so far it was only known for $Z_2$, in which case it equals $2$. We prove that phylogenetic…
The general Markov model of the evolution of biological sequences along a tree leads to a parameterization of an algebraic variety. Understanding this variety and the polynomials, called phylogenetic invariants, which vanish on it, is a…
We define phylogenetic projective toric model of a trivalent graph as a generalization of a binary symmetric model of a trivalent phylogenetic tree. Generators of the pro- jective coordinate ring of the models of graphs with one cycle are…
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…
In algebraic statistics, the Kimura 3-parameter model is one of the most interesting and classical phylogenetic models. We prove that the ideals associated to this model are generated in degree four, confirming a conjecture by Sturmfels and…
Group-based models arise in algebraic statistics while studying evolution processes. They are represented by embedded toric algebraic varieties. Both from the theoretical and applied point of view one is interested in determining the ideals…
Recently there have been several attempts to provide a whole set of generators of the ideal of the algebraic variety associated to a phylogenetic tree evolving under an algebraic model. These algebraic varieties have been proven to be…
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…
Phylogenetic invariants are certain polynomials in the joint probability distribution of a Markov model on a phylogenetic tree. Such polynomials are of theoretical interest in the field of algebraic statistics and they are also of practical…
Any permutation has a disjoint cycle decomposition and concept generates an equivalence class on the symmetry group called the cycle-type. The main focus of this work is on permutations of restricted cycle-types, with particular emphasis on…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
In this article we consider the cycle structure of compositions of pairs of involutions in the symmetric group S_n chosen uniformly at random. These can be modeled as modified 2-regular graphs, giving rise to exponential generating…
A genus one curve of degree 5 is defined by the 4 x 4 Pfaffians of a 5 x 5 alternating matrix of linear forms on P^4. We describe a general method for investigating the invariant theory of such models. We use it to explain how we found our…
Motivated by phylogenetics, our aim is to obtain a system of equations that define a phylogenetic variety on an open set containing the biologically meaningful points. In this paper we consider phylogenetic varieties defined via group-based…
Phylogenetic networks describe the evolution of a set of taxa for which reticulate events have occurred at some point in their evolutionary history. Of particular interest is when the evolutionary history between a set of just three taxa…
Algebraic techniques in phylogenetics have historically been successful at proving identifiability results and have also led to novel reconstruction algorithms. In this paper, we study the ideal of phylogenetic invariants of the…
We continue the analysis of the Modular Isomorphism Problem for $2$-generated $p$-groups with cyclic derived subgroup, $p>2$, started in [D. Garc\'ia-Lucas, \'A. del R\'io, and M. Stanojkovski. On group invariants determined by modular…
A skew morphism of a finite group $B$ is a permutation $\varphi$ of $B$ that preserves the identity element of $B$ and has the property that for every $a\in B$ there exists a positive integer $i_a$ such that $\varphi(ab) =…
Statistical models of evolution are algebraic varieties in the space of joint probability distributions on the leaf colorations of a phylogenetic tree. The phylogenetic invariants of a model are the polynomials which vanish on the variety.…