BBCA: Improving the scalability of *BEAST using random binning

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

Anomalous Unrooted Gene Trees

(2013) James H. Degnan   SYSTEMATIC BIOLOGY

Origin of land plants using the multispecies coalescent model

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

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

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

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

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

Bayesian Inference of Species Trees from Multilocus Data

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

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

BEST: Bayesian estimation of species trees under the coalescent model

(2008) L. Liu   BIOINFORMATICS

Non-homogeneous models of sequence evolution in the Bio++ suite of libraries and programs

(2008) Julien Dutheil et al.   BMC EVOLUTIONARY BIOLOGY

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION