Related papers: The expected value under the Yule model of the squ…
The Shapley value, a solution concept from cooperative game theory, has recently been considered for both unrooted and rooted phylogenetic trees. Here, we focus on the Shapley value of unrooted trees and first revisit the so-called split…
We have developed an alignment-free method that calculates phylogenetic distances using a maximum likelihood approach for a model of sequence change on patterns that are discovered in unaligned sequences. To evaluate the phylogenetic…
Galled trees, directed acyclic graphs that model evolutionary histories with isolated hybridization events, have become very popular due to both their biological significance and the existence of polynomial time algorithms for their…
Phylogenetic inference-the derivation of a hypothesis for the common evolutionary history of a group of species- is an active area of research at the intersection of biology, computer science, mathematics, and statistics. One assumes the…
Let $T$ be a tree with vertex set $\{1, \ldots, n\}$ such that each edge is assigned a nonzero weight. The squared distance matrix of $T,$ denoted by $\Delta,$ is the $n \times n$ matrix with $(i,j)$-element $d(i,j)^2,$ where $d(i,j)$ is…
The subtree prune-and-regraft (SPR) distance metric is a fundamental way of comparing evolutionary trees. It has wide-ranging applications, such as to study lateral genetic transfer, viral recombination, and Markov chain Monte Carlo…
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.…
In order to conduct a statistical analysis on a given set of phylogenetic gene trees, we often use a distance measure between two trees. In a statistical distance-based method to analyze discordance between gene trees, it is a key to decide…
Several indices that measure the degree of balance of a rooted phylogenetic tree have been proposed so far in the literature. In this work we define and study a new index of this kind, which we call the total cophenetic index: the sum, over…
Phylogenetic networks extend phylogenetic trees to model non-vertical inheritance, by which a lineage inherits material from multiple parents. The computational complexity of estimating phylogenetic networks from genome-wide data with…
Predicting the ancestral sequences of a group of homologous sequences related by a phylogenetic tree has been the subject of many studies, and numerous methods have been proposed to this purpose. Theoretical results are available that show…
Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…
Neutral macroevolutionary models, such as the Yule model, give rise to a probability distribution on the set of discrete rooted binary trees over a given leaf set. Such models can provide a signal as to the approximate location of the root…
We establish a limit formula for the median of the distance between two leaves in a fully resolved unrooted phylogenetic tree with n leaves. More precisely, we prove that this median is equal, in the limit, to the square root of 4*ln(2)*n.
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
The study of species organization and their clustering by genetic or phenotypic similarity is carried out with the tools of phylogenetic trees. An important structural property of phylogenetic trees is the balance, which measures how taxa…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
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…
Diversification is nested, and early models suggested this could lead to a great deal of evolutionary redundancy in the Tree of Life. This result is based on a particular set of branch lengths produced by the common coalescent, where…
Dissimilarity measures for (possibly weighted) phylogenetic trees based on the comparison of their vectors of path lengths between pairs of taxa, have been present in the systematics literature since the early seventies. But, as far as…