Simulation-Based Evaluation of Hybridization Network Reconstruction Methods in the Presence of Incomplete Lineage Sorting

A scalability study of phylogenetic network inference methods using empirical datasets and simulations involving a single reticulation

(2016) Hussein A. Hejase et al.   BMC BIOINFORMATICS

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

(2016) Claudia Solís-Lemus et al.   PLoS Genetics

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

Inferring the mode of origin of polyploid species from next-generation sequence data

(2015) Camille Roux et al.   MOLECULAR ECOLOGY

Bears in a Forest of Gene Trees: Phylogenetic Inference Is Complicated by Incomplete Lineage Sorting and Gene Flow

(2014) Verena E. Kutschera et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

The Effective Population Sizes of the Anthropoid Ancestors of the Human-Chimpanzee Lineage Provide Insights on the Historical Biogeography of the Great Apes

(2013) C. G. Schrago   MOLECULAR BIOLOGY AND EVOLUTION

A Versatile and Highly Efficient Toolkit Including 102 Nuclear Markers for Vertebrate Phylogenomics, Tested by Resolving the Higher Level Relationships of the Caudata

(2013) Xing Xing Shen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

(2013) Yun Yu et al.   SYSTEMATIC BIOLOGY

Statistical Inference of Allopolyploid Species Networks in the Presence of Incomplete Lineage Sorting

(2013) Graham Jones et al.   SYSTEMATIC BIOLOGY

Robustness to Divergence Time Underestimation When Inferring Species Trees from Estimated Gene Trees

(2013) Michael DeGiorgio et al.   SYSTEMATIC BIOLOGY

Computational approaches to species phylogeny inference and gene tree reconciliation

(2013) Luay Nakhleh   TRENDS IN ECOLOGY & EVOLUTION

Origin of land plants using the multispecies coalescent model

(2013) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2012) S. Song et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

A Statistical Approach for Distinguishing Hybridization and Incomplete Lineage Sorting

(2009) Simon Joly et al.   AMERICAN NATURALIST

Computing galled networks from real data

(2009) D. H. Huson et al.   BIOINFORMATICS

Inferring polyploid phylogenies from multiply-labeled gene trees

(2009) Martin Lott et al.   BMC EVOLUTIONARY BIOLOGY

Identifying Hybridization Events in the Presence of Coalescence via Model Selection

(2009) Laura Salter Kubatko   SYSTEMATIC BIOLOGY

Properties of Consensus Methods for Inferring Species Trees from Gene Trees

(2009) James H. Degnan et al.   SYSTEMATIC 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

Using supernetworks to distinguish hybridization from lineage-sorting

(2008) Barbara R Holland et al.   BMC EVOLUTIONARY BIOLOGY

Modular networks and cumulative impact of lateral transfer in prokaryote genome evolution

(2008) T. Dagan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Detecting hybrid speciation in the presence of incomplete lineage sorting using gene tree incongruence: A model

(2008) Chen Meng et al.   THEORETICAL POPULATION BIOLOGY

Analysis of 142 genes resolves the rapid diversification of the rice genus

(2008) Xin-Hui Zou et al.   GENOME BIOLOGY