Related papers: Bounding the softwired parsimony score of a phylog…
Construction of phylogenetic trees and networks for extant species from their characters represents one of the key problems in phylogenomics. While solution to this problem is not always uniquely defined and there exist multiple methods for…
Phylogenetic methods typically rely on an appropriate model of how data evolved in order to infer an accurate phylogenetic tree. For molecular data, standard statistical methods have provided an effective strategy for extracting…
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,…
The reconstruction of phylogenetic networks is an important but challenging problem in phylogenetics and genome evolution, as the space of phylogenetic networks is vast and cannot be sampled well. One approach to the problem is to solve the…
One of the main aims of phylogenetics is the reconstruction of the correct evolutionary tree when data concerning the underlying species set are given. These data typically come in the form of DNA, RNA or protein alignments, which consist…
The maximum parsimony phylogenetic tree reconstruction problem is NP-hard, presenting a computational bottleneck for classical computing and motivating the exploration of emerging paradigms like quantum computing. To this end, we design…
Phylogenetic trees canonically arise as embeddings of phylogenetic networks. We recently showed that the problem of deciding if two phylogenetic networks embed the same sets of phylogenetic trees is computationally hard, \blue{in…
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…
The so-called binary perfect phylogeny with persistent characters has recently been thoroughly studied in computational biology as it is less restrictive than the well known binary perfect phylogeny. Here, we focus on the notion of (binary)…
Phylogenetic trees play a key role in the reconstruction of evolutionary relationships. Typically, they are derived from aligned sequence data (like DNA, RNA, or proteins) by using optimization criteria like, e.g., maximum parsimony (MP).…
Given a set $X$ of species, a phylogenetic tree is an unrooted binary tree whose leaves are bijectively labelled by $X$. Such trees can be used to show the way species evolve over time. One way of understanding how topologically different…
The full strong branching (FSB) rule is well known to produce extremely small branch-and-bound trees. This rule guides branching decisions based exclusively on the information regarding local gains in the linear programming (LP) bounds. We…
Phylogenetic networks are generalizations of phylogenetic trees that allow the representation of reticulation events such as horizontal gene transfer or hybridization, and can also represent uncertainty in inference. A subclass of these,…
In this paper, we investigate a conjecture by von Haeseler concerning the Maximum Parsimony method for phylogenetic estimation, which was published by the Newton Institute in Cambridge on a list of open phylogenetic problems in 2007. This…
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…
Rooted phylogenetic networks provide an explicit representation of the evolutionary history of a set $X$ of sampled species. In contrast to phylogenetic trees which show only speciation events, networks can also accommodate reticulate…
Phylogenetic networks have gained prominence over the years due to their ability to represent complex non-treelike evolutionary events such as recombination or hybridization. Popular combinatorial objects used to construct them are triplet…
Phylogenetic trees represent certain species and their likely ancestors. In such a tree, present-day species are leaves and an edge from u to v indicates that u is an ancestor of v. Weights on these edges indicate the phylogenetic distance.…
In phylogenetics, a central problem is to infer the evolutionary relationships between a set of species $X$; these relationships are often depicted via a phylogenetic tree -- a tree having its leaves univocally labeled by elements of $X$…
Phylogenetic networks are necessary to represent the tree of life expanded by edges to represent events such as horizontal gene transfers, hybridizations or gene flow. Not all species follow the paradigm of vertical inheritance of their…