Related papers: Phylogenetic Algebraic Geometry
Tropical algebraic geometry is an active new field of mathematics that establishes and studies some very general principles to translate algebro-geometric problems into purely combinatorial ones. This expository paper gives an introduction…
Phylogenetic trees are binary nonplanar trees with labelled leaves, and plane oriented recursive trees are planar trees with an increasing labelling. Both families are enumerated by double factorials. A bijection is constructed, using the…
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…
Null models of binary phylogenetic trees are useful for testing hypotheses on real world phylogenies. In this paper we consider phylogenies as binary trees without edge lengths together with a sampling measure and encode them as algebraic…
A toric degeneration in algebraic geometry is a process where a given projective variety is being degenerated into a toric one. Then one can obtain information about the original variety via analyzing the toric one, which is a much easier…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
We are interested in shapes of real algebraic curves in the plane and regions surrounded by them: they are named refined algebraic domains by the author. As characteristic finite sets, we consider points contained in two curves and the sets…
Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…
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…
Phylogenetic networks generalise phylogenetic trees and allow for the accurate representation of the evolutionary history of a set of present-day species whose past includes reticulate events such as hybridisation and lateral gene transfer.…
Associated to any graph is a toric ideal whose generators record relations among the cuts of the graph. We study these ideals and the geometry of the corresponding toric varieties. Our theorems and conjectures relate the combinatorial…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
We seek to determine a real algebraic variety from a fixed finite subset of points. Existing methods are studied and new methods are developed. Our focus lies on aspects of topology and algebraic geometry, such as dimension and defining…
Projective geometry provides the preferred framework for most implementations of Euclidean space in graphics applications. Translations and rotations are both linear transformations in projective geometry, which helps when it comes to…
A phylogenetic tree is a way to organize a finite set of species, individuals or other sources of related data. The species for which we have existing DNA data make up the set of leaves of the tree. The balanced minimal evolution method of…
Mostly aimed at an audience with backgrounds in geometry and homological algebra, these notes offer an introduction to derived geometry based on a lecture course given by the second author. The focus is on derived algebraic geometry, mainly…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
The article presents a new approach to euclidean plane geometry based on projective geometric algebra (PGA). It is designed for anyone with an interest in plane geometry, or who wishes to familiarize themselves with PGA. After a brief…
Linear Geometry studies geometric properties which can be expressed via the notion of a line. All information about lines is encoded in a ternary relation called a line relation. A set endowed with a line relation is called a liner. So,…
Modelling the substitution of nucleotides along a phylogenetic tree is usually done by a hidden Markov process. This allows to define a distribution of characters at the leaves of the trees and one might be able to obtain polynomial…