Related papers: A Phylogenetic Trees Analysis of SARS-CoV-2

The evolution of aligned DNA sequence sites is generally modeled by a Markov process operating along the edges of a phylogenetic tree. It is well known that the probability distribution on the site patterns at the tips of the tree…

One approach to estimating a species tree from a collection of gene trees is to first estimate probabilities of clades from the gene trees, and then to construct the species tree from the estimated clade probabilities. While a greedy…

Tree methods (recursive partitioning) are a popular class of nonparametric methods for analyzing data. One extension of the basic tree methodology is the survival tree, which applies recursive partitioning to censored survival data. There…

In evolutionary biology, networks are becoming increasingly used to represent evolutionary histories for species that have undergone non-treelike or reticulate evolution. Such networks are essentially directed acyclic graphs with a leaf set…

In this paper, we consider a tree inference problem motivated by the critical problem in single-cell genomics of reconstructing dynamic cellular processes from sequencing data. In particular, given a population of cells sampled from such a…

Characterising drivers of SARS-CoV-2 circulation is crucial for understanding COVID-19 because of the severity of control measures adopted during the pandemic. Whole genome sequence data augmented with demographic metadata provides the best…

The inference of phylogenetic networks, which model complex evolutionary processes including hybridization and gene flow, remains a central challenge in evolutionary biology. Until now, statistically consistent inference methods have been…

Noise sensitivity of functions on the leaves of a binary tree is studied, and a hypercontractive inequality is obtained. We deduce that the spider walk is not noise stable.

The degree distribution of an ordered tree $T$ with $n$ nodes is $\vec{n} = (n_0,\ldots,n_{n-1})$, where $n_i$ is the number of nodes in $T$ with $i$ children. Let $\mathcal{N}(\vec{n})$ be the number of trees with degree distribution…

An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…

Tree Containment is a fundamental problem in phylogenetics useful for verifying a proposed phylogenetic network, representing the evolutionary history of certain species. Tree Containment asks whether the given phylogenetic tree (for…

Covid-19 infection, which spread to the whole world in December 2019 and is still active, caused more than 250 thousand deaths in the world today. Researches on this subject have been focused on analyzing the genetic structure of the virus,…

Topological phylogenetic trees can be assigned edge weights in several natural ways, highlighting different aspects of the tree. Here the rooted triple and quartet metrizations are introduced, and applied to formulate novel fast methods of…

Rooted plane trees are reduced by four different operations on the fringe. The number of surviving nodes after reducing the tree repeatedly for a fixed number of times is asymptotically analyzed. The four different operations include…

The Sackin and Colless indices are two widely-used metrics for measuring the balance of trees and for testing evolutionary models in phylogenetics. This short paper contributes two results about the Sackin and Colless indices of trees. One…

For a model of molecular evolution to be useful for phylogenetic inference, the topology of evolutionary trees must be identifiable. That is, from a joint distribution the model predicts, it must be possible to recover the tree parameter.…

Tropical rainforests exhibit a rich repertoire of spatial patterns emerging from the intricate relationship between the microscopic interaction between species. In particular, the distribution of vegetation clusters can shed much light on…

A general formulation is presented for continuum scaling limits of stochastic spanning trees. A spanning tree is expressed in this limit through a consistent collection of subtrees, which includes a tree for every finite set of endpoints in…

The metric space of phylogenetic trees defined by Billera, Holmes, and Vogtmann, which we refer to as BHV space, provides a natural geometric setting for describing collections of trees on the same set of taxa. However, it is sometimes…

Let $G$ be a 3-connected planar graph. Define the co-tree of a spanning tree $T$ of $G$ as the graph induced by the dual edges of $E(G)-E(T)$. The well-known cut-cycle duality implies that the co-tree is itself a tree. Let a $k$-tree be a…