In the light of deep coalescence: revisiting trees within networks

On Tree-Based Phylogenetic Networks

(2016) Louxin Zhang   JOURNAL OF COMPUTATIONAL BIOLOGY

Reticulate evolutionary history and extensive introgression in mosquito species revealed by phylogenetic network analysis

(2016) Dingqiao Wen et al.   MOLECULAR ECOLOGY

Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

(2016) Dingqiao Wen et al.   PLoS Genetics

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

Phylogenomic species tree estimation in the presence of incomplete lineage sorting and horizontal gene transfer

(2015) Ruth Davidson et al.   BMC GENOMICS

Conundrum of jumbled mosquito genomes

(2015) A. G. Clark et al.   SCIENCE

Which Phylogenetic Networks are Merely Trees with Additional Arcs?

(2015) Andrew R. Francis et al.   SYSTEMATIC BIOLOGY

Reconstructible Phylogenetic Networks: Do Not Distinguish the Indistinguishable

(2015) Fabio Pardi et al.   PLoS Computational Biology

Maximum likelihood inference of reticulate evolutionary histories

(2014) Yun Yu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Extensive introgression in a malaria vector species complex revealed by phylogenomics

(2014) M. C. Fontaine et al.   SCIENCE

An Algorithm for Constructing Parsimonious Hybridization Networks with Multiple Phylogenetic Trees

(2013) Yufeng Wu   JOURNAL OF COMPUTATIONAL BIOLOGY

Identifying a species tree subject to random lateral gene transfer

(2013) Mike Steel et al.   JOURNAL OF THEORETICAL BIOLOGY

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

Dendroscope 3: An Interactive Tool for Rooted Phylogenetic Trees and Networks

(2012) Daniel H. Huson et al.   SYSTEMATIC BIOLOGY

The Probability of a Gene Tree Topology within a Phylogenetic Network with Applications to Hybridization Detection

(2012) Yun Yu et al.   PLoS Genetics

Phylogenetic networks do not need to be complex: using fewer reticulations to represent conflicting clusters

(2010) Leo van Iersel et al.   BIOINFORMATICS

Locating a tree in a phylogenetic network

(2010) Leo van Iersel et al.   INFORMATION PROCESSING LETTERS

When two trees go to war

(2010) Leo van Iersel et al.   JOURNAL OF THEORETICAL BIOLOGY

Species Tree Inference by Minimizing Deep Coalescences

(2009) Cuong Than et al.   PLoS Computational Biology

PhyloNet: a software package for analyzing and reconstructing reticulate evolutionary relationships

(2008) Cuong Than et al.   BMC BIOINFORMATICS

Seeing the trees and their branches in the network is hard

(2008) Iyad A. Kanj et al.   THEORETICAL COMPUTER SCIENCE