Related papers: Tropical Density Estimation of Phylogenetic Trees
Phylogenetic trees are often constructed by using a metric on the set of taxa that label the leaves of the tree. While there are a number of methods for constructing a tree using a given metric, such trees will only display the metric if it…
Consider a population that is expanding in two-dimensional space. Suppose we collect data from a sample of individuals taken at random either from the entire population, or from near the outer boundary of the population. A quantity of…
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 investigate parameterized algorithms for computing the average-tree phylogenetic diversity (APD) in rooted phylogenetic networks, studying the problem under different structural parameters that capture the deviation of a network from a…
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 consider the problem of estimating the evolutionary history of a set of species (phylogeny or species tree) from several genes. It is known that the evolutionary history of individual genes (gene trees) might be topologically distinct…
The reconstruction of a species phylogeny from genomic data faces two significant hurdles: 1) the trees describing the evolution of each individual gene--i.e., the gene trees--may differ from the species phylogeny and 2) the molecular…
The relative importance of the intrinsic and extrinsic factors determining the variety of geometric shapes exhibited by dendritic trees remains unclear. This question was addressed by developing a model of the growth of dendritic trees…
Phylogenetic trees represent the evolutionary relationships between extant lineages, where extinct or non-sampled lineages are omitted. Extending the work of Stadler and collaborators, this paper focuses on the branch lengths in…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
The Robinson-Foulds (RF) metric is arguably the most widely used measure of phylogenetic tree similarity, despite its well-known shortcomings: For example, moving a single taxon in a tree can result in a tree that has maximum distance to…
Phylogenetic networks are directed acyclic graphs that depict the genomic evolution of related taxa. Reticulation nodes in such networks (nodes with more than one parent) represent reticulate evolutionary events, such as recombination,…
Phylogenetic trees describe the relationships between species in the evolutionary process, and provide information about the rates of diversification. To understand the mechanisms behind macroevolution, we consider a class of multitype…
Given a gene-tree labeled topology $G$ and a species tree $S$, the "ancestral configurations" at an internal node $k$ of $S$ represent the combinatorially different sets of gene lineages that can be present at $k$ when all possible…
Density Estimation Trees (DETs) are decision trees trained on a multivariate dataset to estimate its probability density function. While not competitive with kernel techniques in terms of accuracy, they are incredibly fast, embarrassingly…
Phylogenetic networks are a type of leaf-labelled, acyclic, directed graph used by biologists to represent the evolutionary history of species whose past includes reticulation events. A phylogenetic network is tree-child if each non-leaf…
Modeling multiple sampling densities within a hierarchical framework enables borrowing of information across samples. These density random effects can act as kernels in latent variable models to represent exchangeable subgroups or clusters.…
The asymmetric tropical distance is a distance measure on the tropical torus $\mathbb{R}^n/\mathbb{R}\mathbf{1}$ and in particular on the Bergman fan $B(K_N) \subseteq \mathbb{R}^{\binom{N}{2}}/\mathbb{R}\mathbf{1}$ of the complete…
We consider a broadcasting problem on a tree where a binary digit (e.g., a spin or a nucleotide's purine/pyrimidine type) is propagated from the root to the leaves through symmetric noisy channels on the edges that randomly flip the state…
Given a distance matrix consisting of pairwise distances between species, a distance-based phylogenetic reconstruction method returns a tree metric or equidistant tree metric (ultrametric) that best fits the data. We investigate…