Related papers: Phylogenetic trees and Euclidean embeddings
Phylogenetic networks are a generalisation of phylogenetic trees that allow for more complex evolutionary histories that include hybridisation-like processes. It is of considerable interest whether a network can be considered `tree-like' or…
The ongoing explosion of genome sequence data is transforming how we reconstruct and understand the histories of biological systems. Across biological scales, from individual cells to populations and species, trees-based models provide a…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
Word embeddings are a popular way to improve downstream performances in contemporary language modeling. However, the underlying geometric structure of the embedding space is not well understood. We present a series of explorations using…
In this work, we answer an open problem in the study of phylogenetic networks. Phylogenetic trees are rooted binary trees in which all edges are directed away from the root, whereas phylogenetic networks are rooted acyclic digraphs. For the…
Phylogenetic mixtures model the inhomogeneous molecular evolution commonly observed in data. The performance of phylogenetic reconstruction methods where the underlying data is generated by a mixture model has stimulated considerable recent…
There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression 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…
The reliability of a phylogenetic inference method from genomic sequence data is ensured by its statistical consistency. Bayesian inference methods produce a sample of phylogenetic trees from the posterior distribution given sequence data.…
Understanding the evolution of a set of genes or species is a fundamental problem in evolutionary biology. The problem we study here takes as input a set of trees describing {possibly discordant} evolutionary scenarios for a given set of…
The log-det distance between two aligned DNA sequences was introduced as a tool for statistically consistent inference of a gene tree under simple non-mixture models of sequence evolution. Here we prove that the log-det distance, coupled…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
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…
Evolutionary relationships between species are usually inferred through phylogenetic analysis, which provides phylogenetic trees computed from allelic profiles built by sequencing specific regions of the sequences and abstracting them to…
Tree embedding has been a fundamental method in algorithm design with wide applications. We focus on the efficiency of building tree embedding in various computational settings under high-dimensional Euclidean $\mathbb{R}^d$. We devise a…
A model of genomic sequence evolution on a species tree should include not only a sequence substitution process, but also a coalescent process, since different sites may evolve on different gene trees due to incomplete lineage sorting.…
In 2007, Eickmeyer et al. showed that the tree topologies outputted by the Neighbor-Joining (NJ) algorithm and the balanced minimum evolution (BME) method for phylogenetic reconstruction are each determined by a polyhedral subdivision of…
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…
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…
The evolutionary relationships between species are typically represented in the biological literature by rooted phylogenetic trees. However, a tree fails to capture ancestral reticulate processes, such as the formation of hybrid species or…