Related papers: Non-bifurcating phylogenetic tree inference via th…

Connected acyclic graphs (trees) are data objects that hierarchically organize categories. Collections of trees arise in a diverse variety of fields, including evolutionary biology, public health, machine learning, social sciences and…

Likelihood-based methods are widely considered the best approaches for reconstructing ancestral states. Although much effort has been made to study properties of these methods, previous works often assume that both the tree topology and…

We derive tractable criteria for the consistency of Bayesian tree reconstruction procedures, which constitute a central class of algorithms for inferring common ancestry among DNA sequence samples in phylogenetics. Our results encompass…

Selective inference is considered for testing trees and edges in phylogenetic tree selection from molecular sequences. This improves the previously proposed approximately unbiased test by adjusting the selection bias when testing many trees…

Metagenomics provides a powerful new tool set for investigating evolutionary interactions with the environment. However, an absence of model-based statistical methods means that researchers are often not able to make full use of this…

We introduce inference trees (ITs), a new class of inference methods that build on ideas from Monte Carlo tree search to perform adaptive sampling in a manner that balances exploration with exploitation, ensures consistency, and alleviates…

Motivation: Many inference tools use the Perfect Phylogeny Model (PPM) to learn trees from noisy variant allele frequency (VAF) data. Learning in this setting is hard, and existing tools use approximate or heuristic algorithms. An…

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…

Probabilistic programming frameworks are powerful tools for statistical modelling and inference. They are not immediately generalisable to phylogenetic problems due to the particular computational properties of the phylogenetic tree object.…

Survival analysis studies and predicts the time of death, or other singular unrepeated events, based on historical data, while the true time of death for some instances is unknown. Survival trees enable the discovery of complex nonlinear…

Tree alignment graphs (TAGs) provide an intuitive data structure for storing phylogenetic trees that exhibits the relationships of the individual input trees and can potentially account for nested taxonomic relationships. This paper…

Explanatory variables in a predictive regression typically exhibit low signal strength and various degrees of persistence. Variable selection in such a context is of great importance. In this paper, we explore the pitfalls and possibilities…

Binary phylogenetic trees inferred from biological data are central to understanding the shared history among evolutionary units. However, inferring the placement of latent nodes in a tree is computationally expensive. State-of-the-art…

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,…

Phylogenetic reconstruction aims at finding plausible hypotheses of the evolutionary history of genes or species based on genomic sequence information. The distinction of orthologous genes (genes that having a common ancestry and diverged…

Bayesian inference is a popular and widely-used approach to infer phylogenies (evolutionary trees). However, despite decades of widespread application, it remains difficult to judge how well a given Bayesian Markov chain Monte Carlo (MCMC)…

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…

The branching structure of biological evolution confers statistical dependencies on phenotypic trait values in related organisms. For this reason, comparative macroevolutionary studies usually begin with an inferred phylogeny that describes…

Estimating phylogenetic trees is an important problem in evolutionary biology, environmental policy and medicine. Although trees are estimated, their uncertainties are discarded by mathematicians working in tree space. Here we explicitly…

The inability to resolve deep node relationships of highly divergent/rapidly evolving protein families is a major factor that stymies evolutionary studies. In this manuscript, we propose a Multiple Sequence Alignment (MSA) independent…