Related papers: Phylogenetic tree distance computation over succin…
Phylogenetic diversity indices are commonly used to rank the elements in a collection of species or populations for conservation purposes. The derivation of these indices is typically based on some quantitative description of the…
Phylogenetic tree comparison metrics are an important tool in the study of evolution, and hence the definition of such metrics is an interesting problem in phylogenetics. In a paper in Taxon fifty years ago, Sokal and Rohlf proposed to…
The problem of reconstructing evolutionary trees or phylogenies is of great interest in computational biology. A popular model for this problem assumes that we are given the set of leaves (current species) of an unknown binary tree and the…
Within the field of phylogenetics there is great interest in distance measures to quantify the dissimilarity of two trees. Recently, a new distance measure has been proposed: the Maximum Parsimony (MP) distance. This is based on the…
Phylogenetic tree inference using deep DNA sequencing is reshaping our understanding of rapidly evolving systems, such as the within-host battle between viruses and the immune system. Densely sampled phylogenetic trees can contain special…
When estimating a phylogeny from a multiple sequence alignment, researchers often assume the absence of recombination. However, if recombination is present, then tree estimation and all downstream analyses will be impacted, because…
The statistical estimation of phylogenies is always associated with uncertainty, and accommodating this uncertainty is an important component of modern phylogenetic comparative analysis. The birth-death polytomy resolver is a method of…
Phylogenetics is a branch of computational biology that studies the evolutionary relationships among biological entities. Its long history and numerous applications notwithstanding, inference of phylogenetic trees from sequence data remains…
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 problem of comparing trees representing the evolutionary histories of cancerous tumors has turned out to be crucial, since there is a variety of different methods which typically infer multiple possible trees. A departure from the…
We consider the following basic problem in phylogenetic tree construction. Let $\mathcal{P} = \{T_1, \ldots, T_k\}$ be a collection of rooted phylogenetic trees over various subsets of a set of species. The tree compatibility problem asks…
We introduce a new phylogenetic reconstruction algorithm which, unlike most previous rigorous inference techniques, does not rely on assumptions regarding the branch lengths or the depth of the tree. The algorithm returns a forest which is…
The method of flexi-Weighted Least Squares on evolutionary trees uses simple polynomial or exponential functions of the evolutionary distance in place of model-based variances. This has the advantage that unexpected deviations from…
Agreement forests continue to play a central role in the comparison of phylogenetic trees since their introduction more than 25 years ago. More specifically, they are used to characterise several distances that are based on tree…
Many popular algorithms for searching the space of leaf-labelled trees are based on tree rearrangement operations. Under any such operation, the problem is reduced to searching a graph where vertices are trees and (undirected) edges are…
Phylogenetic diversity is a measure for describing how much of an evolutionary tree is spanned by a subset of species. If one applies this to the (unknown) subset of current species that will still be present at some future time, then this…
Phylogenetic trees are leaf-labelled trees, where the leaves correspond to extant species (taxa), and the internal vertices represent ancestral species. The evolutionary history of a set of species can be explained by more than one…
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…
Phylogenetic networks which are, as opposed to trees, suitable to describe processes like hybridization and horizontal gene transfer, play a substantial role in evolutionary research. However, while non-treelike events need to be taken into…
The number of the non-shared edges of two phylogenies is a basic measure of the dissimilarity between the phylogenies. The non-shared edges are also the building block for approximating a more sophisticated metric called the nearest…