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

A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing

(2013) John E. McCormack et al.   PLoS One

Species formation and geographical range evolution in a genus of Central American cloud forest salamanders (Dendrotriton)

(2012) Sean M. Rovito et al.   JOURNAL OF BIOGEOGRAPHY

iGLASS: An Improvement to the GLASS Method for Estimating Species Trees from Gene Trees

(2012) Ethan M. Jewett et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Improvements to a Class of Distance Matrix Methods for Inferring Species Trees from Gene Trees

(2012) Laura J. Helmkamp et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy

(2012) L. Lacey Knowles et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Species Tree Estimation for the Late Blight Pathogen, Phytophthora infestans, and Close Relatives

(2012) Jaime E. Blair et al.   PLoS One

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

Pleistocene Speciation in the Genus Populus (Salicaceae)

(2012) Nicholas D. Levsen 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

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

(2011) Yufeng Wu   EVOLUTION

Applications of next-generation sequencing to phylogeography and phylogenetics

(2011) John E. McCormack et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2011) Yun Yu et al.   SYSTEMATIC BIOLOGY

Inferring Species-Level Phylogenies and Taxonomic Distinctiveness Using Multilocus Data in Sistrurus Rattlesnakes

(2011) Laura S. Kubatko et al.   SYSTEMATIC BIOLOGY

Simulating Trees with a Fixed Number of Extant Species

(2011) Tanja Stadler   SYSTEMATIC BIOLOGY

SuperFine: Fast and Accurate Supertree Estimation

(2011) M. Shel Swenson et al.   SYSTEMATIC BIOLOGY

Phybase: an R package for species tree analysis

(2010) L. Liu et al.   BIOINFORMATICS

A maximum pseudo-likelihood approach for estimating species trees under the coalescent model

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

SpedeSTEM: a rapid and accurate method for species delimitation

(2010) DANIEL D. ENCE et al.   Molecular Ecology Resources

Rapid and accurate species tree estimation for phylogeographic investigations using replicated subsampling

(2010) Sarah Hird et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

(2010) Huateng Huang et al.   SYSTEMATIC BIOLOGY

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

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

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

(2009) Laura S. Kubatko et al.   BIOINFORMATICS

Incomplete Lineage Sorting: Consistent Phylogeny Estimation from Multiple Loci

(2009) E. Mossel et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Maximum tree: a consistent estimator of the species tree

(2009) Liang Liu et al.   JOURNAL OF MATHEMATICAL BIOLOGY

Bayesian Inference of Species Trees from Multilocus Data

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

What Is the Danger of the Anomaly Zone for Empirical Phylogenetics?

(2009) Huateng Huang et al.   SYSTEMATIC BIOLOGY

Species Trees from Highly Incongruent Gene Trees in Rice

(2009) Karen A. Cranston et al.   SYSTEMATIC BIOLOGY

Maximum Likelihood Estimates of Species Trees: How Accuracy of Phylogenetic Inference Depends upon the Divergence History and Sampling Design

(2009) John E. McCormack et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu 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

Estimation of Hominoid Ancestral Population Sizes under Bayesian Coalescent Models Incorporating Mutation Rate Variation and Sequencing Errors

(2008) Ralph Burgess et al.   MOLECULAR BIOLOGY AND EVOLUTION