Related papers: Bounding the softwired parsimony score of a phylog…
Distance-based phylogenetic algorithms attempt to solve the NP-hard least squares phylogeny problem by mapping an arbitrary dissimilarity map representing biological data to a tree metric. The set of all dissimilarity maps is a Euclidean…
One of the main aims in phylogenetics is the estimation of ancestral sequences based on present-day data like, for instance, DNA alignments. One way to estimate the data of the last common ancestor of a given set of species is to first…
Phylogenetic (evolutionary) trees and networks are leaf-labeled graphs that are widely used to represent the evolutionary relationships between entities such as species, languages, cancer cells, and viruses. To reconstruct and analyze…
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…
Phylogenetic networks are graphs that are used to represent evolutionary relationships between different taxa. They generalize phylogenetic trees since for example, unlike trees, they permit lineages to combine. Recently, there has been…
We prove that Nakhleh's latest dissimilarity measure for phylogenetic networks is a metric on the classes of tree-child phylogenetic networks, of semi-binary time consistent tree-sibling phylogenetic networks, and of multi-labeled…
Machine learning is increasingly used to guide branch-and-cut (B&C) for mixed-integer linear programming by learning score-based policies for selecting branching variables and cutting planes. Many approaches train on local signals from…
The structure of an evolving network contains information about its past. Extracting this information efficiently, however, is, in general, a difficult challenge. We formulate a fast and efficient method to estimate the most likely history…
Phylogenetic networks are a generalization of phylogenetic trees that are used to represent non-tree-like evolutionary histories that arise in organisms such as plants and bacteria, or uncertainty in evolutionary histories. An…
An important problem in evolutionary biology is to reconstruct the evolutionary history of a set $X$ of species. This history is often represented as a phylogenetic network, that is, a connected graph with leaves labelled by elements in $X$…
Phylogenetic networks provide a way to describe and visualize evolutionary histories that have undergone so-called reticulate evolutionary events such as recombination, hybridization or horizontal gene transfer. The level k of a network…
Most of major algorithms for phylogenetic tree reconstruction assume that sequences in the analyzed set either do not have any offspring, or that parent sequences can maximally mutate into just two descendants. The graph resulting from such…
Recently, there has been much interest in finding globally optimal Bayesian network structures. These techniques were developed for generative scores and can not be directly extended to discriminative scores, as desired for classification.…
Motivation: The abundance of gene flow in the Tree of Life challenges the notion that evolution can be represented with a fully bifurcating process, as this process cannot capture important biological realities like hybridization,…
A phylogenetic network is a directed acyclic graph that visualises an evolutionary history containing so-called reticulations such as recombinations, hybridisations or lateral gene transfers. Here we consider the construction of a simplest…
Phylogenetically decisive collections of taxon sets have the property that if trees are chosen for each of their elements, as long as these trees are compatible, the resulting supertree is unique. This means that as long as the trees…
We systematically study the computational complexity of a broad class of computational problems in phylogenetic reconstruction. The class contains for example the rooted triple consistency problem, forbidden subtree problems, the quartet…
We describe a kernel of size 9k-8 for the NP-hard problem of computing the Tree Bisection and Reconnect (TBR) distance k between two unrooted binary phylogenetic trees. We achieve this by extending the existing portfolio of reduction rules…
Many classes of phylogenetic networks have been proposed in the literature. A feature of several of these classes is that if one restricts a network in the class to a subset of its leaves, then the resulting network may no longer lie within…
The study of Markov processes and broadcasting on trees has deep connections to a variety of areas including statistical physics, graphical models, phylogenetic reconstruction, Markov Chain Monte Carlo, and community detection in random…