Related papers: Phylogenetic invariants for group-based models
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…
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…
A phylogenetic variety is an algebraic variety parameterized by a statistical model of the evolution of biological sequences along a tree. Understanding this variety is an important problem in the area of algebraic statistics with…
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 prove identifiability of the tree parameters of the 3-class Jukes-Cantor mixture model. The proof uses ideas from algebraic statistics, in particular: finding phylogenetic invariants that separate the varieties associated to different…
We study phylogenetic invariants of models of evolution whose group of symmetries is the cyclic group with 3 elements. We prove that projective schemes corresponding to the ideal I of phylogenetic invariants of such a model and to its…
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…
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.…
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…
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…
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…
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…
The purpose of this article is to show how the isotropy subgroup of leaf permutations on binary trees can be used to systematically identify tree-informative invariants relevant to models of phylogenetic evolution. In the quartet case, we…
Phylogenetic networks can represent evolutionary events that cannot be described by phylogenetic trees, such as hybridization, introgression, and lateral gene transfer. Studying phylogenetic networks under a statistical model of DNA…
We address the problem of studying the toric ideals of phylogenetic invariants for a general group-based model on an arbitrary claw tree. We focus on the group $\mathbb Z_2$ and choose a natural recursive approach that extends to other…
Buczy\'{n}ska and Wi\'{s}niewski showed that for the Jukes Cantor binary model of a 3-valent tree the Hilbert polynomial depends only on the number of leaves of the tree and not on its shape. We ask if this can be generalized to other…
In this paper we present geometric features of group based models. We focus on the 3-Kimura model. We present a precise geometric description of the variety associated to any tree on a Zariski open set. In particular this set contains all…
Changing base composition during the evolution of biological sequences can mislead some of the phylogenetic inference techniques in current use. However, detecting whether such a process has occurred may be difficult, since convergent…
The reconstruction of phylogenetic trees from molecular sequence data relies on modelling site substitutions by a Markov process, or a mixture of such processes. In general, allowing mixed processes can result in different tree topologies…
In the last decade, some algebraic tools have been successfully applied to phylogenetic reconstruction. These tools are mainly based on the knowledge of equations describing algebraic varieties associated to phylogenetic trees evolving…