Related papers: Phylogenetic degrees for claw trees
The goal of the work is to implement molecular phylogenetic calculations using the Grid paradigm by means of the MrBayes software using Directed Acyclic Graphs (DAG) jobs. In this method, a set of jobs depends on the input or the output of…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
In mathematical phylogenetics, the time-consistent galled trees provide a simple class of rooted binary network structures that can be used to represent a variety of different biological phenomena. We study the enumerative combinatorics of…
Leaves, i.e., vertices of degree one, can play a significant role in graph structure, especially in sparsely connected settings in which leaves often constitute the largest fraction of vertices. We consider a leaf-based counterpart of the…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
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…
In this paper, we provide a polynomial time algorithm to calculate the probability of a {\it ranked} gene tree topology for a given species tree, where a ranked tree topology is a tree topology with the internal vertices being ordered. The…
The Kimura 3-parameter model on a tree of n leaves is one of the most used in phylogenetics. The affine algebraic variety W associated to it is a toric variety. We study its geometry and we prove that it is isomorphic to a geometric…
The structural constants of an evolution algebra is given by a quadratic matrix $A$. In this work we establish equivalence between nil, right nilpotent evolution algebras and evolution algebras, which are defined by upper triangular matrix…
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…
In this thesis we study toric degenerations of projective varieties. We compare different constructions to understand how and why they are related as s first step towards developing a global framework. In focus are toric degenerations…
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…
Phylogenetic species trees typically represent the speciation history as a bifurcating tree. Speciation events that simultaneously create more than two descendants, thereby creating polytomies in the phylogeny, are possible. Moreover, the…
Phylogenetic comparative methods are well established tools for using inter-species variation to analyse phenotypic evolution and adaptation. They are generally hampered, however, by predominantly univariate approaches and failure to…
Recently, much attention has been given to understanding recombination events along a chromosome in a variety of field. For instance, many population genetics problems are limited by the inaccuracy of inferred evolutionary histories of…
The reconstruction of phylogenies from DNA or protein sequences is a major task of computational evolutionary biology. Common phenomena, notably variations in mutation rates across genomes and incongruences between gene lineage histories,…
A phylogenetic tree shows the evolutionary relationships among species. Internal nodes of the tree represent speciation events and leaf nodes correspond to species. A goal of phylogenetics is to combine such trees into larger trees, called…
Phylogenetic networks are a generalization of phylogenetic trees that allow for the representation of non-treelike evolutionary events, like recombination, hybridization, or lateral gene transfer. In this paper, we present and study a new…
Directed acyclic graphical models (DAGs) are often used to describe common structural properties in a family of probability distributions. This paper addresses the question of classifying DAGs up to an isomorphism. By considering Gaussian…
Evolutionary histories for species that cross with one another or exchange genetic material can be represented by leaf-labelled, directed graphs called phylogenetic networks. A major challenge in the burgeoning area of phylogenetic networks…