Related papers: Confidence sets for phylogenetic trees
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…
The spread of infectious disease in a human community or the proliferation of fake news on social media can be modeled as a randomly growing tree-shaped graph. The history of the random growth process is often unobserved but contains…
In stopping the spread of infectious diseases, pathogen genomic data can be used to reconstruct transmission events and characterize population-level sources of infection. Most approaches for identifying transmission pairs do not account…
The aim of this review is to present and analyze the probabilistic models of mathematical phylogenetics which have been intensively used in recent years in biology as the cornerstone of attempts to infer and reconstruct the ancestral…
A large class of phylogenetic networks can be obtained from trees by the addition of horizontal edges between the tree edges. These networks are called tree based networks. Reticulation-visible networks and child-sibling networks are all…
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.…
Phylogenetic networks are an extension of phylogenetic trees which are used to represent evolutionary histories in which reticulation events (such as recombination and hybridization) have occurred. A central question for such networks is…
Latent space models for network data characterize each node through a vector of latent features whose pairwise similarities define the edge probabilities among the pairs of nodes. Although this formulation has led to successful…
In this paper we present a new way to understand the timing of branching events in phylogenetic trees. Our method explicitly considers the relative timing of diversification events between sister clades; as such it is complimentary to…
An important problem in phylogenetics is the construction of phylogenetic trees. One way to approach this problem, known as the supertree method, involves inferring a phylogenetic tree with leaves consisting of a set $X$ of species from a…
The PHASE software package allows phylogenetic tree construction with a number of evolutionary models designed specifically for use with RNA sequences that have conserved secondary structure. Evolution in the paired regions of RNAs occurs…
A contemporary and fundamental problem faced by many evolutionary biologists is how to puzzle together a collection $\mathcal P$ of partial trees (leaf-labelled trees whose leaves are bijectively labelled by species or, more generally,…
The way to infer well-supported phylogenetic trees that precisely reflect the evolutionary process is a challenging task that completely depends on the way the related core genes have been found. In previous computational biology studies,…
Tree-based phylogenetic networks, which may be roughly defined as leaf-labeled networks built by adding arcs only between the original tree edges, have elegant properties for modeling evolutionary histories. We answer an open question of…
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…
Large Language Models (LLMs) are accelerating scientific idea generation, but rigorously evaluating these numerous, often superficial, AI-generated propositions for novelty and factual accuracy is a critical bottleneck; manual verification…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees relating species. Along branches, sequence evolution is modelled using a continuous-time Markov process characterised by an instantaneous rate…
Identifying viral pathogens and characterizing their transmission is essential to developing effective public health measures in response to a pandemic. Phylogenetics, though currently the most popular tool used to characterize the likely…
Phylogenetic trees are widely used to display estimates of how groups of species evolved. Each phylogenetic tree can be seen as a collection of clusters, subgroups of the species that evolved from a common ancestor. When phylogenetic trees…
In evolutionary biology, phylogenetic trees are commonly inferred from a set of characters (partitions) of a collection of biological entities (e.g., species or individuals in a population). Such characters naturally arise from molecular…