Related papers: Genomic data analysis in tree spaces

This article presents a new way to understand the descriptive ability of tree shape statistics. Where before tree shape statistics were chosen by their ability to distinguish between macroevolutionary models, the ``resolution'' presented in…

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…

Viruses evolve in the background of host immune systems that exert selective pressure and drive viral evolutionary trajectories. This interaction leads to different evolutionary patterns in antigenic space. Examples observed in nature…

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…

We destroy a finite tree of size $n$ by cutting its edges one after the other and in uniform random order. Informally, the associated cut-tree describes the genealogy of the connected components created by this destruction process. We…

Defining the energy function as the negative logarithm of the density, we explore the energy landscape of a distribution via the tree of sublevel sets of its energy. This tree represents the hierarchy among the connected components of the…

The Dollo model for reconstructing evolutionary trees from binary characters has been proposed as a generalization of the infinite sites model, also known as the Perfect Phylogeny. In particular, the Dollo model is considered more realistic…

Molecular phylogeny has focused mainly on improving models for the reconstruction of gene trees based on sequence alignments. Yet, most phylogeneticists seek to reveal the history of species. Although the histories of genes and species are…

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…

In this work we analyze the evolution of voluntary vaccination in networked populations by entangling the spreading dynamics of an influenza-like disease with an evolutionary framework taking place at the end of each influenza season so…

Possibility to establish macroscopic phenomenological theory for biological systems, akin to the akin to the well-established framework of thermodynamics, is briefly reviewed. We introduce the concept of an evolutionary fluctuation-response…

Whole genome sequencing of pathogens from multiple hosts in an epidemic offers the potential to investigate who infected whom with unparalleled resolution, potentially yielding important insights into disease dynamics and the impact of…

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…

The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…

Phylogenetics begins with reconstructing biological family trees from genetic data. Since Nature is not limited to tree-like histories, we use networks to organize our data, and have discovered new polytopes, metric spaces, and simplicial…

We consider neutral evolution of a large population subject to changes in its population size. For a population with a time-variable carrying capacity we have computed the distributions of the total branch lengths of its sample genealogies.…

We present a new method for exploring cancer gene expression data based on tools from algebraic topology. Our method selects a small relevant subset from tens of thousands of genes while simultaneously identifying nontrivial higher order…

We observe $n$ sequences at each of $m$ sites, and assume that they have evolved from an ancestral sequence that forms the root of a binary tree of known topology and branch lengths, but the sequence states at internal nodes are unknown.…

The reconstruction of large phylogenetic trees from data that violates clocklike evolution (or as a supertree constructed from any m input trees) raises a difficult question for biologists - how can one assign relative dates to the vertices…

Evolutionary relationships between species are represented by phylogenetic trees, but these relationships are subject to uncertainty due to the random nature of evolution. A geometry for the space of phylogenetic trees is necessary in order…