Related papers: A Phylogenetic Trees Analysis of SARS-CoV-2
Each gene has its own evolutionary history which can substantially differ from the evolutionary histories of other genes. For example, some individual genes or operons can be affected by specific horizontal gene transfer and recombination…
We study the growth of a time-ordered rooted tree by probabilistic attachment of new vertices to leaves. We construct a likelihood function of the leaves based on the connectivity of the tree. We take such connectivity to be induced by the…
Tree-based networks are a class of phylogenetic networks that attempt to formally capture what is meant by "tree-like" evolution. A given non-tree-based phylogenetic network, however, might appear to be very close to being tree-based, or…
Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…
Ultrametric matrices are a class of covariance matrices that arise in latent tree models. As a parameter space in a statistical model, the set of ultrametric matrices is neither convex nor a smooth manifold. Focus in the literature has…
Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…
Applying a method to reconstruct a phylogenetic tree from random data provides a way to detect whether that method has an inherent bias towards certain tree `shapes'. For maximum parsimony, applied to a sequence of random 2-state data, each…
A genus one labeled circle tree is a tree with its vertices on a circle, such that together they can be embedded in a surface of genus one, but not of genus zero. We define an e-reduction process whereby a special type of subtree, called an…
Dynamic trees are mixtures of tree structured belief networks. They solve some of the problems of fixed tree networks at the cost of making exact inference intractable. For this reason approximate methods such as sampling or mean field…
A Supertree synthesizes the topologies of a set of phylogenetic trees carrying overlapping taxa set. In process, conflicts in the tree topologies are aimed to be resolved with the consensus clades. Such a problem is proved to be NP-hard.…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Since Darwin, species trees have been used as a simplified description of the relationships which summarize the complicated network $N$ of reality. Recent evidence of hybridization and lateral gene transfer, however, suggest that there are…
The reconstruction of phylogenetic trees based on viral genetic sequence data sequentially sampled from an epidemic provides estimates of the past transmission dynamics, by fitting epidemiological models to these trees. To our knowledge,…
Deciding whether there is a single tree -a supertree- that summarizes the evolutionary information in a collection of unrooted trees is a fundamental problem in phylogenetics. We consider two versions of this question: agreement and…
Any algebraic connection on a vector bundle on a smooth complex algebraic curve determines an irregular class and in turn a fission tree at each puncture. The fission trees are the discrete data classifying the admissible deformation…
In the critical beta-splitting model of a random $n$-leaf rooted tree, clades are recursively (from the root) split into sub-clades, and a clade of $m$ leaves is split into sub-clades containing $i$ and $m-i$ leaves with probabilities…
Phylogenetic trees are simple models of evolutionary processes. They describe conditionally independent divergent evolution of taxa from common ancestors. Phylogenetic trees commonly do not have enough flexibility to adequately model all…
Several classification methods assume that the underlying distributions follow tree-structured graphical models. Indeed, trees capture statistical dependencies between pairs of variables, which may be crucial to attain low classification…
An evolutionary tree is a cascade of bifurcations starting from a single common root, generating a growing set of daughter species as time goes by. Species here is a general denomination for biological species, spoken languages or any other…
We study the evolution of branching trees embedded in Euclidean spaces with suppressed branching of spatially close nodes. This cooperative branching process accounts for the effect of overcrowding of nodes in the embedding space and mimics…