Phylogenetic networks are models of the evolution of a set of organisms that generalize phylogenetic trees. By allowing the existence of reticulation events (such as recombination, hybridization, or horizontal gene transfer), the model is no longer a tree but a directed acyclic graph (DAG). We consider the problem of finding a phylogenetic network to model a set of sequences of molecular data, ...

The aim of this study was to determine the distribution of lung diseases in the autopsy subjects brought for medicolegal examination in the Transkei area. Two hundred histopathological slides were examined microscopically. Of them, 46 subjects (23%) showed some kind of pathology. There were four kinds of lesions observed: dust reticulation (anthracosis), necrotizing granulomatous inflammation, ...

UNLABELLED T-REX (tree and reticulogram reconstruction) is an application to reconstruct phylogenetic trees and reticulation networks from distance matrices. The application includes a number of tree fitting methods like NJ, UNJ or ADDTREE which have been very popular in phylogenetic analysis. At the same time, the software comprises several new methods of phylogenetic analysis such as: tree re...

Reticulate evolutionary processes result in phylogenetic histories that cannot be modeled using a tree topology. Here, we apply methods from topological data analysis to molecular sequence data with reticulations. Using a simple example, we demonstrate the correspondence between nontrivial higher homology and reticulate evolution. We discuss the sensitivity of the standard filtration and show c...

Phylogenetic networks are models of evolution that go beyond trees, incorporating non-tree-like biological events such as recombination (or more generally reticulation), which occur either in a single species (meiotic recombination) or between species (reticulation due to lateral gene transfer and hybrid speciation). The central algorithmic problems are to reconstruct a plausible history of mut...