Naive binning improves phylogenomic analyses

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

Estimating Optimal Species Trees from Incomplete Gene Trees Under Deep Coalescence

(2012) MD. Shamsuzzoha Bayzid et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

Fast and accurate methods for phylogenomic analyses

(2011) Jimmy Yang et al.   BMC BIOINFORMATICS

Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles

(2011) Yun Yu et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Consistency Properties of Species Tree Inference by Minimizing Deep Coalescences

(2011) Cuong V. Than et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer

(2011) Yujin Chung et al.   SYSTEMATIC BIOLOGY

BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis

(2010) Bret R. Larget et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

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

Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

(2009) Michael DeGiorgio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Bayesian Inference of Species Trees from Multilocus Data

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

Estimating Species Trees: Methods of Phylogenetic Analysis When There Is Incongruence across Genes

(2009) L. Lacey Knowles   SYSTEMATIC BIOLOGY

Properties of Consensus Methods for Inferring Species Trees from Gene Trees

(2009) James H. Degnan et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

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

(2008) Cuong Than et al.   BMC BIOINFORMATICS

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION