Related papers: Computational Tools for Evaluating Phylogenetic an…
Metrics on rooted phylogenetic trees are integral to a number of areas of phylogenetic analysis. Cluster-similarity metrics have recently been introduced in order to limit skew in the distribution of distances, and to ensure that trees in…
Cancers follow a clonal Darwinian evolution, with fitter subclones replacing more quiescent cells, ultimately giving rise to macroscopic disease. High-throughput genomics provides the opportunity to investigate these processes and determine…
Staged tree models enhance Bayesian networks by incorporating context-specific dependencies through a stage-based structure. In this study, we present a new framework for estimating staged trees using hierarchical clustering on the…
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…
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…
Phylogenetic inference can potentially result in a more accurate tree using data from multiple loci. However, if the loci are incongruent--due to events such as incomplete lineage sorting or horizontal gene transfer--it can be misleading to…
This paper considers metric spaces where distances between a pair of nodes are represented by distance intervals. The goal is to study methods for the determination of hierarchical clusters, i.e., a family of nested partitions indexed by a…
Clustering is a fundamental approach to understanding data patterns, wherein the intuitive Euclidean distance space is commonly adopted. However, this is not the case for implicit cluster distributions reflected by qualitative attribute…
Combining a set of phylogenetic trees into a single phylogenetic network that explains all of them is a fundamental challenge in evolutionary studies. Existing methods are computationally expensive and can either handle only small numbers…
Phylogenetic trees are a central tool in understanding evolution. They are typically inferred from sequence data, and capture evolutionary relationships through time. It is essential to be able to compare trees from different data sources…
Motivation: The construction of statistics for summarizing posterior samples returned by a Bayesian phylogenetic study has so far been hindered by the poor geometric insights available into the space of phylogenetic trees, and ad hoc…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
When solving ill-posed inverse problems, one often desires to explore the space of potential solutions rather than be presented with a single plausible reconstruction. Valuable insights into these feasible solutions and their associated…
We describe the use of the Frechet mean and variance in the Billera-Holmes-Vogtmann (BHV) treespace to summarize and explore the diversity of a set of phylogenetic trees. We show that the Frechet mean is comparable to other summary methods,…
Billera-Holmes-Vogtmann (BHV) tree space is a geodesic metric space of edge-weighted phylogenetic trees with a fixed leaf set. Constructing parametric distributions on this space is challenging due to its non-Euclidean geometry and the…
Merge trees are fundamental structures in topological data analysis. Interleaving distance is a widely accepted metric for comparing merge trees, with applications in visualization and scientific computing. While a greedy algorithm exists…
Phylogenetic trees in genetics and biology in general are all binary. We make an attempt to answer one fundamental question: Is such binary branching from the coarsest to the finest scales sustained by data? We convert this question into an…
This paper investigates the computational geometry relevant to calculations of the Frechet mean and variance for probability distributions on the phylogenetic tree space of Billera, Holmes and Vogtmann, using the theory of probability…
Inferring the phylogenetic relationships among a sample of organisms is a fundamental problem in modern biology. While distance-based hierarchical clustering algorithms achieved early success on this task, these have been supplanted by…
Rapid developments in genetics and biology have led to phylogenetic methods becoming an important direction in the study of cancer and viral evolution. Although our understanding of gene biology and biochemistry has increased and is…