Related papers: Using the tangle: a consistent construction of phy…
Tree structures appear in many fields of the life sciences, including phylogenetics, developmental biology and nucleic acid structures. Trees can be used to represent RNA secondary structures, which directly relate to the function of…
Tree comparison metrics have proven to be an invaluable aide in the reconstruction and analysis of phylogenetic (evolutionary) trees. The path-length distance between trees is a particularly attractive measure as it reflects differences in…
We define, analyze, and give efficient algorithms for two kinds of distance measures for rooted and unrooted phylogenies. For rooted trees, our measures are based on the topologies the input trees induce on triplets; that is, on…
Phylogenetic trees summarize evolutionary relationships between organisms, and tools to analyze collections of phylogenetic trees enable contrasts between different genes' ancestry. The BHV metric space has enabled the analysis of…
In evolutionary biology, phylogenetic networks are constructed to represent the evolution of species in which reticulate events are thought to have occurred, such as recombination and hybridization. It is therefore useful to have…
We propose a novel method for the inference of phylogenetic trees that utilises point configurations on hyperbolic space as its optimisation landscape. Each taxon corresponds to a point of the point configuration, while the evolutionary…
We consider the problem of estimating species trees from unrooted gene tree topologies in the presence of incomplete lineage sorting, a common phenomenon that creates gene tree heterogeneity in multilocus datasets. One popular class of…
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…
More than ever, today we are left with the abundance of molecular data outpaced by the advancements of the phylogenomic methods. Especially in the case of presence of many genes over a set of species under the phylogeny question, more…
It is possible to consider stochastic models of sequence evolution in phylogenetics in the context of a dynamical tensor description inspired from physics. Approaching the problem in this framework allows for the well developed methods of…
This paper introduces constNJ, the first algorithm for phylogenetic reconstruction of sets of trees with constrained pairwise rooted subtree-prune regraft (rSPR) distance. We are motivated by the problem of constructing sets of trees which…
Phylogenetic trees can be reconstructed from the matrix which contains the distances between all pairs of languages in a family. Recently, we proposed a new method which uses normalized Levenshtein distances among words with same meaning…
Phylogenetic trees are leaf-labelled trees used to model the evolution of species. In practice it is not uncommon to obtain two topologically distinct trees for the same set of species, and this motivates the use of distance measures to…
Merge trees are a common topological descriptor for data with a hierarchical component, such as terrains and scalar fields. The interleaving distance, in turn, is a common distance for comparing merge trees. However, the interleaving…
Phylogenetic tree reconstruction is traditionally based on multiple sequence alignments (MSAs) and heavily depends on the validity of this information bottleneck. With increasing sequence divergence, the quality of MSAs decays quickly.…
Recently there has been renewed interest in phylogenetic inference methods based on phylogenetic invariants, alongside the related Markov invariants. Broadly speaking, both these approaches give rise to polynomial functions of sequence site…
In this paper we examine the usefulness of two classes of algorithms Distance Methods, Discrete Character Methods (Felsenstein and Felsenstein 2003) widely used in genetics, for predicting the family relationships among a set of related…
Phylogenetic networks are a generalization of phylogenetic trees that are used in biology to represent reticulate or non-treelike evolution. Recently, several algorithms have been developed which aim to construct phylogenetic networks from…
The distance matrix of a dataset $X$ of $n$ points with respect to a distance function $f$ represents all pairwise distances between points in $X$ induced by $f$. Due to their wide applicability, distance matrices and related families of…
Phylogenetic networks are generalizations of trees that allow for the modeling of non-tree like evolutionary processes. Split networks give a useful way to construct networks with intuitive distance structures induced from the associated…