Bayesian Inference of Reticulate Phylogenies under the Multispecies Network Coalescent

Inferring Phylogenetic Networks with Maximum Pseudolikelihood under Incomplete Lineage Sorting

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

Estimating phylogenetic trees from genome-scale data

(2015) Liang Liu et al.   Annals of the New York Academy of Sciences

How reticulated are species?

(2015) James Mallet et al.   BIOESSAYS

A maximum pseudo-likelihood approach for phylogenetic networks

(2015) Yun Yu et al.   BMC GENOMICS

Conundrum of jumbled mosquito genomes

(2015) A. G. Clark et al.   SCIENCE

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

Ancient hybridizations among the ancestral genomes of bread wheat

(2014) T. Marcussen et al.   SCIENCE

Extensive introgression in a malaria vector species complex revealed by phylogenomics

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

Fast algorithms and heuristics for phylogenomics under ILS and hybridization

(2013) Yun Yu et al.   BMC BIOINFORMATICS

Parsimonious Inference of Hybridization in the Presence of Incomplete Lineage Sorting

(2013) Yun Yu 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

Networks: expanding evolutionary thinking

(2013) Eric Bapteste et al.   TRENDS IN GENETICS

Inferring Species Trees Directly from Biallelic Genetic Markers: Bypassing Gene Trees in a Full Coalescent Analysis

(2012) David Bryant et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2012) Yun Yu et al.   PLoS Genetics

Fast computation of minimum hybridization networks

(2011) Benjamin Albrecht et al.   BIOINFORMATICS

COALESCENT-BASED SPECIES TREE INFERENCE FROM GENE TREE TOPOLOGIES UNDER INCOMPLETE LINEAGE SORTING BY MAXIMUM LIKELIHOOD

(2011) Yufeng Wu   EVOLUTION

Coalescent Histories on Phylogenetic Networks and Detection of Hybridization Despite Incomplete Lineage Sorting

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

Close lower and upper bounds for the minimum reticulate network of multiple phylogenetic trees

(2010) Yufeng Wu   BIOINFORMATICS

STEM: species tree estimation using maximum likelihood for gene trees under coalescence

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Bayesian Inference of Species Trees from Multilocus Data

(2009) J. Heled et al.   MOLECULAR BIOLOGY AND EVOLUTION

Coalescent methods for estimating phylogenetic trees

(2009) Liang Liu et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework

(2009) Erik W. Bloomquist et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

(2009) James H. Degnan et al.   TRENDS IN ECOLOGY & EVOLUTION

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

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

(2008) Cuong Than et al.   BMC BIOINFORMATICS

The role of hybridization in evolution

(2003) N. H. Barton   MOLECULAR ECOLOGY