NetRAX: accurate and fast maximum likelihood phylogenetic network inference

S Lutteropp, C Scornavacca, AM Kozlov, B Morel… - …, 2022 - academic.oup.com
Motivation Phylogenetic networks can represent non-treelike evolutionary scenarios.
Current, actively developed approaches for phylogenetic network inference jointly account …

[HTML][HTML] Inferring phylogenetic networks from multifurcating trees via cherry picking and machine learning

G Bernardini, L van Iersel, E Julien, L Stougie - … phylogenetics and evolution, 2024 - Elsevier
The Hybridization problem asks to reconcile a set of conflicting phylogenetic trees into a
single phylogenetic network with the smallest possible number of reticulation nodes. This …

Advancing admixture graph estimation via maximum likelihood network orientation

EK Molloy, A Durvasula, S Sankararaman - Bioinformatics, 2021 - academic.oup.com
Motivation Admixture, the interbreeding between previously distinct populations, is a
pervasive force in evolution. The evolutionary history of populations in the presence of …

Comparing the topology of phylogenetic network generators

R Janssen, P Liu - Journal of bioinformatics and computational …, 2021 - World Scientific
Phylogenetic networks represent evolutionary history of species and can record natural
reticulate evolutionary processes such as horizontal gene transfer and gene recombination …

Counting phylogenetic networks of level 1 and 2

M Bouvel, P Gambette, M Mansouri - Journal of mathematical biology, 2020 - Springer
Phylogenetic networks generalize phylogenetic trees, and have been introduced in order to
describe evolution in the case of transfer of genetic material between coexisting species …

RF-Net 2: Fast inference of virus reassortment and hybridization networks

A Markin, S Wagle, TK Anderson, O Eulenstein - Bioinformatics, 2022 - academic.oup.com
Motivation A phylogenetic network is a powerful model to represent entangled evolutionary
histories with both divergent (speciation) and convergent (eg hybridization, reassortment …

Generating normal networks via leaf insertion and nearest neighbor interchange

L Zhang - BMC bioinformatics, 2019 - Springer
Background Galled trees are studied as a recombination model in theoretical population
genetics. This class of phylogenetic networks has been generalized to tree-child networks …

Exploring spaces of semi-directed level-1 networks

S Linz, K Wicke - Journal of Mathematical Biology, 2023 - Springer
Semi-directed phylogenetic networks have recently emerged as a class of phylogenetic
networks sitting between rooted (directed) and unrooted (undirected) phylogenetic networks …

The burning number of directed graphs: bounds and computational complexity

R Janssen - arxiv preprint arxiv:2001.03381, 2020 - arxiv.org
The burning number of a graph was recently introduced by Bonato et al. Although they
mention that the burning number generalises naturally to directed graphs, no further …

Treewidth of display graphs: bounds, brambles and applications

R Janssen, M Jones, S Kelk, G Stamoulis… - arxiv preprint arxiv …, 2018 - arxiv.org
Phylogenetic trees and networks are leaf-labelled graphs used to model evolution. Display
graphs are created by identifying common leaf labels in two or more phylogenetic trees or …