ASTRAL: genome-scale coalescent-based species tree estimation

Land plant origins and coalescence confusion

(2014) Mark S. Springer et al.   TRENDS IN PLANT SCIENCE

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Identifying localized biases in large datasets: A case study using the avian tree of life

(2013) Rebecca T. Kimball et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

Phylogenomic Analyses of Nuclear Genes Reveal the Evolutionary Relationships within the BEP Clade and the Evidence of Positive Selection in Poaceae

(2013) Lei Zhao et al.   PLoS One

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

(2013) Michael DeGiorgio et al.   SYSTEMATIC BIOLOGY

Anomalous Unrooted Gene Trees

(2013) James H. Degnan   SYSTEMATIC BIOLOGY

Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales

(2013) Brian Tilston Smith et al.   SYSTEMATIC BIOLOGY

Origin of land plants using the multispecies coalescent model

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

Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)

(2012) Ylenia Chiari et al.   BMC BIOLOGY

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

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

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

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Identifying the rooted species tree from the distribution of unrooted gene trees under the coalescent

(2010) Elizabeth S. Allman et al.   JOURNAL OF MATHEMATICAL 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

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

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION