Related papers: Bounding the softwired parsimony score of a phylog…

Identifying a subset of taxa that maximizes Phylogenetic Diversity (PD) is a cornerstone of quantitative conservation planning. Traditionally, PD is defined over a phylogenetic tree in which leaves resemble present-day taxa and the branch…

Reconstructing a parsimonious phylogenetic network that displays multiple phylogenetic trees is an important problem in theory of phylogenetics, where the complexity of the inferred networks is measured by reticulation numbers. The…

Phylogenetic trees and networks are graphs used to model evolutionary relationships, with trees representing strictly branching histories and networks allowing for events in which lineages merge, called reticulation events. While the…

Phylogenetic networks are leaf-labelled directed acyclic graphs that are used to describe non-treelike evolutionary histories and are thus a generalization of phylogenetic trees. The hybridization number of a phylogenetic network is the sum…

Reconciling a gene tree with a species tree is an important task that reveals much about the evolution of genes, genomes, and species, as well as about the molecular function of genes. A wide array of computational tools have been devised…

'Tree-based' phylogenetic networks proposed by Francis and Steel have attracted much attention of theoretical biologists in the last few years. At the heart of the definitions of tree-based phylogenetic networks is the notion of 'support…

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…

Rooted phylogenetic networks provide a more complete representation of the ancestral relationship between species than phylogenetic trees when reticulate evolutionary processes are at play. One way to reconstruct a phylogenetic network is…

Invariants for complicated objects such as those arising in phylogenetics, whether they are invariants as matrices, polynomials, or other mathematical structures, are important tools for distinguishing and working with such objects. In this…

There are several tools available to infer phylogenetic trees, which depict the evolutionary relationships among biological entities such as viral and bacterial strains in infectious outbreaks, or cancerous cells in tumor progression trees.…

The Tree of Life is the graphical structure that represents the evolutionary process from single-cell organisms at the origin of life to the vast biodiversity we see today. Reconstructing this tree from genomic sequences is challenging due…

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…

This paper studies a Markov chain for phylogenetic reconstruction which uses a popular transition between tree topologies known as subtree pruning-and-regrafting (SPR). We analyze the Markov chain in the simpler setting that the generating…

A normal network is uniquely determined by the set of phylogenetic trees that it displays. Given a set $\mathcal{P}$ of rooted binary phylogenetic trees, this paper presents a polynomial-time algorithm that reconstructs the unique binary…

In the context of reconstructing phylogenetic networks from a collection of phylogenetic trees, several characterisations and subsequently algorithms have been established to reconstruct a phylogenetic network that collectively embeds all…

Reticulate evolution can be modelled using phylogenetic networks. Tree-based networks, which are one of the more general classes of phylogenetic networks, have recently gained eminence for its ability to represent evolutionary histories…

Rooted phylogenetic networks are used to describe evolutionary histories that contain non-treelike evolutionary events such as hybridization and horizontal gene transfer. In some cases, such histories can be described by a phylogenetic…

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…

Maximum likelihood is one of the most widely used techniques to infer evolutionary histories. Although it is thought to be intractable, a proof of its hardness has been lacking. Here, we give a short proof that computing the maximum…

Inference of phylogenetic networks is of increasing interest in the genomic era. However, the extent to which phylogenetic networks are identifiable from various types of data remains poorly understood, despite its crucial role in…