Related papers: Laplacian Matrices for Extremely Balanced and Unba…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
This paper investigates spectral properties of the deformed Laplacian matrix, which merges the Laplacian and signless Laplacian matrices of a graph through a one-parameter family of matrices. We present general results on the eigenvalues of…
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…
Tree balance plays an important role in phylogenetics and other research areas, which is why several indices to measure tree balance have been introduced over the years. Nevertheless, a formal definition of what a balance index actually is…
As an alternative to parsimony analyses, stochastic models have been proposed (Lewis, 2001), (Nylander, et al., 2004) for morphological characters, so that maximum likelihood or Bayesian analyses may be used for phylogenetic inference. A…
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…
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,…
It is known from the algebraic graph theory that if $L$ is the Laplacian matrix of some tree $G$ with a vertex degree sequence $\mathbf{d}=(d_1, ..., d_n)^\top$ and $D$ is its distance matrix, then…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
The search for similarity and dissimilarity measures on phylogenetic trees has been motivated by the computation of consensus trees, the search by similarity in phylogenetic databases, and the assessment of clustering results in…
For two decades, the Colless index has been the most frequently used statistic for assessing the balance of phylogenetic trees. In this article, this statistic is studied under the Yule and uniform model of phylogenetic trees. The main tool…
As researchers collect increasingly large molecular data sets to reconstruct the Tree of Life, the heterogeneity of signals in the genomes of diverse organisms poses challenges for traditional phylogenetic analysis. A class of phylogenetic…
Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…
Upper and lower estimates of eigenvalues of the Laplacian on a metric graph have been established in 2017 by G. Berkolaiko, J.B. Kennedy, P. Kurasov and D. Mugnolo. Both these estimates can be achieved at the same time only by highly…
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…
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…
The Laplacian matrix of a simple graph is the difference of the diagonal matrix of vertex degree and the (0,1) adjacency matrix. In the past decades, the Laplacian spectrum has received much more and more attention, since it has been…
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…
We consider the reconciliation problem, in which the task is to find a mapping of a gene tree into a species tree, so as to maximize the likelihood of such fitting, given the available data. We describe a model for the evolution of the…
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.…