Related papers: Epidemic reconstruction in a phylogenetics framewo…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Generative models derived from large protein sequence alignments define complex fitness landscapes, but their utility for accurately modeling non-equilibrium evolutionary dynamics remains unclear. In this work, we perform a rigorous…
A wide range of applications and research has been done with genome-scale metabolic models. In this work we describe a methodology for comparing metabolic networks constructed from genome-scale metabolic models and how to apply this…
Inferring evolutionary histories (phylogenetic trees) has important applications in biology, criminology and public health. However, phylogenetic trees are complex mathematical objects that reside in a non-Euclidean space, which complicates…
Galled trees are studied as a recombination model in population genetics. This class of phylogenetic networks is generalized into tree-child, galled and reticulation-visible network classes by relaxing a structural condition imposed on…
A consensus tree is a phylogenetic tree that synthesizes a given collection of phylogenetic trees, all of which share the same leaf labels but may have different topologies, typically obtained through bootstrapping. Our research focuses on…
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.…
Understanding propagation structures in graph diffusion processes, such as epidemic spread or misinformation diffusion, is a fundamental yet challenging problem. While existing methods primarily focus on source localization, they cannot…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
In phylogenetics, evolution is traditionally represented in a tree-like manner. However, phylogenetic networks can be more appropriate for representing evolutionary events such as hybridization, horizontal gene transfer, and others. In…
Cultural phylogenies, or "trees" of culture, are typically built using methods from biology that use similarities and differences in artifacts to infer the historical relationships between the populations that produced them. While these…
In this paper, we consider the problem of reconstructing trees from traces in the tree edit distance model. Previous work by Davies et al. (2019) analyzed special cases of reconstructing labeled trees. In this work, we significantly expand…
Phylogenetics uses alignments of molecular sequence data to learn about evolutionary trees. Substitutions in sequences are modelled through a continuous-time Markov process, characterised by an instantaneous rate matrix, which standard…
Phylogenetic networks extend phylogenetic trees to allow for modeling reticulate evolutionary processes such as hybridization. They take the shape of a rooted, directed, acyclic graph, and when parameterized with evolutionary parameters,…
PEACH Tree is an easy-to-use, online tool for displaying multiple sequence alignments and phylogenetic trees side-by-side. PEACH Tree is powerful for rapidly tracing evolutionary and transmission histories by filtering invariant sites out…
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…
We develop a new Markov chain on graph partitions that makes relatively global moves yet is computationally feasible to be used as the proposal in the Metropolis-Hastings method. Our resulting algorithm can be made reversible and able to…
We present a contact-based model to study the spreading of epidemics by means of extending the dynamic message passing approach to temporal networks. The shift in perspective from node- to edge-centric quantities enables accurate modelling…
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 trees elucidate evolutionary relationships among species, but phylogenetic inference remains challenging due to the complexity of combining continuous (branch lengths) and discrete parameters (tree topology). Traditional Markov…