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Phylogenetic networks are often constructed by merging multiple conflicting phylogenetic signals into a directed acyclic graph. It is interesting to explore whether a network constructed in this way induces biologically-relevant…
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 learning the structure of undirected graphical models with bounded treewidth, within the maximum likelihood framework. This is an NP-hard problem and most approaches consider local search techniques. In this…
We compare the phylogenetic tensors for various trees and networks for two, three and four taxa. If the probability spaces between one tree or network and another are not identical then there will be phylogenetic tensors that could have…
The maximum/minimum bisection problems are, given an edge-weighted graph, to find a bipartition of the vertex set into two sets whose sizes differ by at most one, such that the total weight of edges between the two sets is…
Good representations for phylogenetic trees and networks are important for optimizing storage efficiency and implementation of scalable methods for the inference and analysis of evolutionary trees for genes, genomes and species. We…
Bayesian inference is now a leading technique for reconstructing phylogenetic trees from aligned sequence data. In this short note, we formally show that the maximum posterior tree topology provides a statistically consistent estimate of a…
We show that there exists a constant $c>0$ such that every $n$-vertex tree $T$ with $\Delta(T)\le cn$ has Ramsey number $R(T)=\max\{t_1+2t_2,2t_1\}-1$, where $t_1\ge t_2$ are the sizes of the bipartition classes of $T$. This improves an…
Computational inference of dated evolutionary histories relies upon various hypotheses about RNA, DNA, and protein sequence mutation rates. Using mutation rates to infer these dated histories is referred to as molecular clock assumption.…
Phylogenetic networks are used to display the relationship of different species whose evolution is not treelike, which is the case, for instance, in the presence of hybridization events or horizontal gene transfers. Tree inference methods…
The treedepth of a graph $G$ is the least possible depth of an elimination forest of $G$: a rooted forest on the same vertex set where every pair of vertices adjacent in $G$ is bound by the ancestor/descendant relation. We propose an…
Billey et al. [arXiv:1507.04976] have recently discovered a surprisingly simple formula for the number $a_n(\sigma)$ of leaf-labelled rooted non-embedded binary trees (also known as phylogenetic trees) with $n\geq 1$ leaves, fixed (for the…
Phylogenetic trees are widely used to understand the evolutionary history of organisms. Tree shapes provide information about macroevolutionary processes. However, macroevolutionary models are unreliable for inferring the true processes…
Given an $n$-point metric space $(X,d_X)$, a tree cover $\mathcal{T}$ is a set of $|\mathcal{T}|=k$ trees on $X$ such that every pair of vertices in $X$ has a low-distortion path in one of the trees in $\mathcal{T}$. Tree covers have been…
A phylogenetic tree is a graphical representation of an evolutionary history of taxa in which the leaves correspond to the taxa and the non-leaves correspond to speciations. One of important problems in phylogenetic analysis is to assemble…
For a phylogenetic tree, the phylogenetic diversity of a set A of taxa is the total weight of edges on paths to A. Finding small sets of maximal diversity is crucial for conservation planning, as it indicates where limited resources can be…
We propose a new succinct representation of labeled trees which represents a tree T using |T|H_k(T) number of bits (plus some smaller order terms), where |T|H_k(T) denotes the k-th order (tree label) entropy, as defined by Ferragina at al.…
A geophylogeny is a phylogenetic tree (or dendrogram) where each leaf (e.g. biological taxon) has an associated geographic location (site). To clearly visualize a geophylogeny, the tree is typically represented as a crossing-free drawing…
The ancestral maximum-likelihood and phylogeography problems are two fundamental problems involving evolutionary studies. The ancestral maximum-likelihood problem involves identifying a rooted tree alongside internal node sequences that…
We investigate a network growth model in which the genealogy controls the evolution. In this model, a new node selects a random target node and links either to this target node, or to its parent, or to its grandparent, etc; all nodes from…