Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies

Species tree estimation using ASTRAL: how many genes are enough?

(2017) Shubhanshu Shekhar et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Fragmentary Gene Sequences Negatively Impact Gene Tree and Species Tree Reconstruction

(2017) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

On the importance of homology in the age of phylogenomics

(2017) Mark S. Springer et al.   SYSTEMATICS AND BIODIVERSITY

Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies

(2016) Erfan Sayyari et al.   MOLECULAR BIOLOGY AND EVOLUTION

New deep-sea species of Xenoturbella and the position of Xenacoelomorpha

(2016) Greg W. Rouse et al.   NATURE

Xenacoelomorpha is the sister group to Nephrozoa

(2016) Johanna Taylor Cannon et al.   NATURE

Inconsistency of Species Tree Methods under Gene Flow

(2016) Claudia Solís-Lemus et al.   SYSTEMATIC BIOLOGY

The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

(2016) Alexander Suh   ZOOLOGICA SCRIPTA

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

A quantum leap in avian biology

(2015) Leo Joseph et al.   EMU

SimPhy: Phylogenomic Simulation of Gene, Locus, and Species Trees

(2015) Diego Mallo et al.   SYSTEMATIC BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Phylotranscriptomic analysis of the origin and early diversification of land plants

(2014) Norman J. Wickett et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Statistical binning enables an accurate coalescent-based estimation of the avian tree

(2014) S. Mirarab et al.   SCIENCE

Whole-genome analyses resolve early branches in the tree of life of modern birds

(2014) E. D. Jarvis et al.   SCIENCE

Anomalous Unrooted Gene Trees

(2013) James H. Degnan   SYSTEMATIC BIOLOGY

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

Phylogenetic Signal and Noise: Predicting the Power of a Data Set to Resolve Phylogeny

(2012) Jeffrey P. Townsend et al.   SYSTEMATIC BIOLOGY

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

(2010) Bret R. Larget et al.   BIOINFORMATICS

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

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

INDELible: A Flexible Simulator of Biological Sequence Evolution

(2009) W. Fletcher 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

Introns outperform exons in analyses of basal avian phylogeny using clathrin heavy chain genes

(2008) Jena L. Chojnowski et al.   GENE

A Dirty Dozen: Twelve P-Value Misconceptions

(2008) Steven Goodman   SEMINARS IN HEMATOLOGY