Related papers: Confidence sets for phylogenetic trees
Phylogenetic trees summarize evolutionary relationships. The Billera-Holmes-Vogtmann (BHV) space for comparing phylogenetic trees has many elegant mathematical properties, but it does not encompass trees with differing leaf sets. To…
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…
The Persistent-Phylogeny Model is an extension of the widely studied Perfect-Phylogeny Model, encompassing a broader range of evolutionary phenomena. Biological and algorithmic questions concerning persistent phylogeny have been intensely…
Phylogenetic tree shapes capture fundamental signatures of evolution. We consider ``ranked'' tree shapes, which are equipped with a total order on the internal nodes compatible with the tree graph. Recent work has established an elegant…
Phylogenetic trees and networks are leaf-labelled graphs that are used to describe evolutionary histories of species. The Tree Containment problem asks whether a given phylogenetic tree is embedded in a given phylogenetic network. Given a…
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…
Accurate identification of synergistic treatment combinations and their underlying biological mechanisms is critical across many disease domains, especially cancer. In translational oncology research, preclinical systems such as…
Phylogenetic networks are a type of directed acyclic graph that represent how a set $X$ of present-day species are descended from a common ancestor by processes of speciation and reticulate evolution. In the absence of reticulate evolution,…
A classic problem in computational biology is constructing a phylogenetic tree given a set of distances between n species. In most cases, a tree structure is too constraining. We consider a circular split network, a generalization of a tree…
Most phylogenetic models assume that the evolutionary process is stationary and reversible. As a result, the root of the tree cannot be inferred as part of the analysis because the likelihood of the data does not depend on the position of…
Understanding which phenotypic traits are consistently correlated throughout evolution is a highly pertinent problem in modern evolutionary biology. Here, we propose a multivariate phylogenetic latent liability model for assessing the…
Although the role of lateral gene transfer is well recognized in the evolution of bacteria, it is generally assumed that it has had less influence among eukaryotes. To explore this hypothesis we compare the dynamics of genome evolution in…
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…
The multispecies coalescent process models the genealogical relationships of genes sampled from several species, enabling useful predictions about phenomena such as the discordance between the gene tree and the species phylogeny due to…
A central problem in biology is to understand how organisms evolve and adapt to their environment by acquiring variations in the observable characteristics or traits of species across the tree of life. With the growing availability of…
Introgression is an evolutionary process in which genes or other types of genetic material are introduced into a genome. It is an important evolutionary process that can, for example, play a fundamental role in speciation. Recently the…
As part of work to connect phylogenetics with machine learning, there has been considerable recent interest in vector encodings of phylogenetic trees. We present a simple new "ordered leaf attachment" (OLA) method for uniquely encoding a…
Construction of phylogenetic trees has traditionally focused on binary trees where all species appear on leaves, a problem for which numerous efficient solutions have been developed. Certain application domains though, such as viral…
Gene trees are evolutionary trees representing the ancestry of genes sampled from multiple populations. Species trees represent populations of individuals -- each with many genes -- splitting into new populations or species. The coalescent…
Many biological studies involve inferring the evolutionary history of a sample of individuals from a large population and interpreting the reconstructed tree. Such an ascertained tree typically represents only a small part of a…