Related papers: A new balance index for phylogenetic trees
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
We introduce a notion of finite sampling consistency for phylogenetic trees and show that the set of finitely sampling consistent and exchangeable distributions on n leaf phylogenetic trees is a polytope. We use this polytope to show that…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
Phylogenetic Diversity (PD) is a prominent quantitative measure of the biodiversity of a collection of present-day species (taxa). This measure is based on the evolutionary distance among the species in the collection. Loosely speaking, if…
Phylogenetics is now fundamental in life sciences, providing insights into the earliest branches of life and the origins and spread of epidemics. However, finding suitable phylogenies from the vast space of possible trees remains…
The path-difference metric is one of the oldest distances for the comparison of fully resolved phylogenetic trees, but its statistical properties are still quite unknown. In this paper we compute the mean value of the square of the…
When we apply comparative phylogenetic analyses to genome data, it is a well-known problem and challenge that some of given species (or taxa) often have missing genes. In such a case, we have to impute a missing part of a gene tree from a…
Tree balance has received considerable attention in recent years, both in phylogenetics and in other areas. Numerous (im)balance indices have been proposed to quantify the (im)balance of rooted trees. A recent comprehensive survey…
Rooted phylogenetic networks allow biologists to represent evolutionary relationships between present-day species by revealing ancestral speciation and hybridization events. A convenient and well-studied class of such networks are…
A topological index reflects the physical, chemical and structural properties of a molecule, and its study has an important role in molecular topology, chemical graph theory and mathematical chemistry. It is a natural problem to…
Phylogenetic trees describe the evolutionary history of a group of present-day species from a common ancestor. These trees are typically reconstructed from aligned DNA sequence data. In this paper we analytically address the following…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
Species tree estimation is a complex problem, due to the fact that different parts of the genome can have different evolutionary histories than the genome itself. One of the causes for this discord is incomplete lineage sorting (also called…
A number of hook formulas and hook summation formulas have previously appeared, involving various classes of trees. One of these classes of trees is rooted trees with labelled vertices, in which the labels increase along every chain from…
Balanced minimum evolution is a distance-based criterion for the reconstruction of phylogenetic trees. Several algorithms exist to find the optimal tree with respect to this criterion. One approach is to minimize a certain linear functional…
A phylogenetic tree is a tree with a fixed set of leaves that has no vertices of degree two. In this paper, we axiomatically define four other discrete structures on the set of leaves. We prove that each of these structures is an equivalent…
A chief problem in phylogenetics and database theory is the computation of a maximum consistent tree from a set of rooted or unrooted trees. A standard input are triplets, rooted binary trees on three leaves, or quartets, unrooted binary…
We introduce a simple algorithm for reconstructing phylogenies from multiple gene trees in the presence of incomplete lineage sorting, that is, when the topology of the gene trees may differ from that of the species tree. We show that our…
A phylogenetic tree is an acyclic graph with distinctly labeled leaves, whose internal edges have a positive weight. Given a set of n leaves, the collection of all phylogenetic trees with this leaf set can be assembled into a metric cube…