Related papers: Leaping through tree space: continuous phylogeneti…
A popular line of research in evolutionary biology is the use of time-calibrated phylogenies for the inference of diversification processes. This requires computing the likelihood of a given ultrametric tree as the reconstructed tree…
Ultrametric trees are trees whose leaves lie at the same distance from the root. They are used to model the genealogy of a population of particles co-existing at the same point in time. We show how the boundary of an ultrametric tree, like…
Bayesian Markov chain Monte Carlo explores tree space slowly, in part because it frequently returns to the same tree topology. An alternative strategy would be to explore tree space systematically, and never return to the same topology. In…
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 selection of the most suitable evolutionary model to analyze the given molecular data is usually left to biologist's choice. In his famous book, J Felsenstein suggested that certain linear equations satisfied by the expected…
Designing flexible probabilistic models over tree topologies is important for developing efficient phylogenetic inference methods. To do that, previous works often leverage the similarity of tree topologies via hand-engineered heuristic…
The presence of reticulate evolutionary events in phylogenies turn phylogenetic trees into phylogenetic networks. These events imply in particular that there may exist multiple evolutionary paths from a non-extant species to an extant one,…
Phylogenetic trees constitute an interesting class of objects for stochastic processes due to the non-standard nature of the space they inhabit. In particular, many statistical applications require the construction of Markov processes on…
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…
Structural information of phylogenetic tree topologies plays an important role in phylogenetic inference. However, finding appropriate topological structures for specific phylogenetic inference tasks often requires significant design effort…
Bayesian phylogenetic inference is currently done via Markov chain Monte Carlo (MCMC) with simple proposal mechanisms. This hinders exploration efficiency and often requires long runs to deliver accurate posterior estimates. In this paper,…
Phylogenies (ancestry trees) depict the evolutionary history of an evolving population. In evolutionary computing, a phylogeny can reveal how an evolutionary algorithm steers a population through a search space, illuminating the…
One approach in phylogenomics to infer the tree of life is based on concatenated multiple sequence alignments from many genes. Unfortunately, the resulting so-called supermatrix is usually sparse, that is, not every gene sequence is…
Rooted phylogenetic networks are used by biologists to infer and represent complex evolutionary relationships between species that cannot be accurately explained by a phylogenetic tree. Tree-child networks are a particular class of rooted…
Bayesian inference for phylogenetics is a gold standard for computing distributions of phylogenies. It faces the challenging problem of. moving throughout the high-dimensional space of trees. However, hyperbolic space offers a low…
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…
The amount of completely sequenced chloroplast genomes increases rapidly every day, leading to the possibility to build large scale phylogenetic trees of plant species. Considering a subset of close plant species defined according to their…
Interpretability is crucial for doctors, hospitals, pharmaceutical companies and biotechnology corporations to analyze and make decisions for high stakes problems that involve human health. Tree-based methods have been widely adopted for…
A classical result, fundamental to evolutionary biology, states that an edge-weighted tree $T$ with leaf set $X$, positive edge weights, and no vertices of degree 2 can be uniquely reconstructed from the set of leaf-to-leaf distances…
A central theme in phylogenetics is the reconstruction and analysis of evolutionary trees from a given set of data. To determine the optimal search methods for reconstructing trees, it is crucial to understand the size and structure of the…