Related papers: Species Trees Forcing Parsimony to Fail
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…
A metric phylogenetic tree relating a collection of taxa induces weighted rooted triples and weighted quartets for all subsets of three and four taxa, respectively. New intertaxon distances are defined that can be calculated from these…
We study the number of distance queries needed to identify certain properties of a hidden tree $T$ on $n$ vertices. A distance query consists of two vertices $x,y$, and the answer is the distance of $x$ and $y$ in $T$. We determine the…
The paper attempts to validate the effectiveness of tree classifiers to classify tabla strokes especially the ones which are overlapping in nature. It uses decision tree, ID3 and random forest as classifiers. A custom made data sets of 650…
This paper extends the study of fringe trees in random plane trees with a given degree statistic. While previous work established the asymptotic normality of the count of fringe trees isomorphic to a fixed tree, we investigate the case…
One can often make inferences about a growing network from its current state alone. For example, it is generally possible to determine how a network changed over time or pick among plausible mechanisms explaining its growth. In practice,…
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.…
Given overlapping subsets of a set of taxa (e.g. species), and posterior distributions on phylogenetic tree topologies for each of these taxon sets, how can we infer a posterior distribution on phylogenetic tree topologies for the entire…
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…
With advances in sequencing technologies, there are now massive amounts of genomic data from across all life, leading to the possibility that a robust Tree of Life can be constructed. However, "gene tree heterogeneity", which is when…
We look for partition theorems for large subtrees for suitable uncountable trees and colourings. We concentrate on sub-trees of $^{\kappa \ge} 2$ expanded by a well ordering of each level. Unlike earlier works, we do not ask the embedding…
Given a graph, we can form a spanning forest by first sorting the edges in some order, and then only keep edges incident to a vertex which is not incident to any previous edge. The resulting forest is dependent on the ordering of the edges,…
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…
Motivation: Millions of genes in the modern species belong to only thousands of `gene families'. A gene family includes instances of the same gene in different species (orthologs) and duplicate genes in the same species (paralogs). Genes…
Over some types of trees with a given number of vertices, which trees minimize or maximize the total number of subtrees or leaf containing subtrees are studied. Here are some of the main results:\ (1)\, Sharp upper bound on the total number…
An evolutionary tree is a rooted tree where each internal vertex has at least two children and where the leaves are labeled with distinct symbols representing species. Evolutionary trees are useful for modeling the evolutionary history of…
Tropical geometry with the max-plus algebra has been applied to statistical learning models over tree spaces because geometry with the tropical metric over tree spaces has some nice properties such as convexity in terms of the tropical…
The classic Maxwell formula calculates the length of a planar locally minimal binary tree in terms of coordinates of its boundary vertices and directions of incoming edges. However, if an extreme tree with a given topology and a boundary…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
We propose a statistical method to test whether two phylogenetic trees with given alignments are significantly incongruent. Our method compares the two distributions of phylogenetic trees given by the input alignments, instead of comparing…