Genome-wide interrogation advances resolution of recalcitrant groups in the tree of life

A Genome-Scale Investigation of How Sequence, Function, and Tree-Based Gene Properties Influence Phylogenetic Inference

(2016) Xing-Xing Shen et al.   Genome Biology and Evolution

The effects of subsampling gene trees on coalescent methods applied to ancient divergences

(2016) Mark P. Simmons et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Implementing and testing the multispecies coalescent model: A valuable paradigm for phylogenomics

(2016) Scott V. Edwards et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The gene tree delusion

(2016) Mark S. Springer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics for Systematic Biology

(2016) David Posada   SYSTEMATIC BIOLOGY

Capturing protein-coding genes across highly divergent species

(2016) Chenhong Li et al.   BIOTECHNIQUES

A comparative study of SVDquartets and other coalescent-based species tree estimation methods

(2015) Jed Chou et al.   BMC GENOMICS

Irrational exuberance for resolved species trees

(2015) Matthew W. Hahn et al.   EVOLUTION

A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing

(2015) Richard O. Prum et al.   NATURE

Correction for Song et al., Resolving conflict in eutherian mammal phylogeny using phylogenomics and the multispecies coalescent model

(2015)   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genomic data do not support comb jellies as the sister group to all other animals

(2015) Davide Pisani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rapid genome reshaping by multiple-gene loss after whole-genome duplication in teleost fish suggested by mathematical modeling

(2015) Jun Inoue et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Response to Comment on "Statistical binning enables an accurate coalescent-based estimation of the avian tree"

(2015) S. Mirarab et al.   SCIENCE

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

(2015) L. Liu et al.   SCIENCE

On the Robustness to Gene Tree Estimation Error (or lack thereof) of Coalescent-Based Species Tree Methods

(2015) Sebastien Roch et al.   SYSTEMATIC BIOLOGY

Selecting Question-Specific Genes to Reduce Incongruence in Phylogenomics: A Case Study of Jawed Vertebrate Backbone Phylogeny

(2015) Meng-Yun Chen et al.   SYSTEMATIC BIOLOGY

The Dynamics of Incomplete Lineage Sorting across the Ancient Adaptive Radiation of Neoavian Birds

(2015) Alexander Suh et al.   PLOS BIOLOGY

Weighted Statistical Binning: Enabling Statistically Consistent Genome-Scale Phylogenetic Analyses

(2015) Md Shamsuzzoha Bayzid et al.   PLoS One

Animal Phylogeny and Its Evolutionary Implications

(2014) Casey W. Dunn et al.   Annual Review of Ecology Evolution and Systematics

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

ExaBayes: Massively Parallel Bayesian Tree Inference for the Whole-Genome Era

(2014) Andre J. Aberer et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenetic analysis at deep timescales: Unreliable gene trees, bypassed hidden support, and the coalescence/concatalescence conundrum

(2014) John Gatesy et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

EVOLUTIONARY ORIGIN AND EARLY BIOGEOGRAPHY OF OTOPHYSAN FISHES (OSTARIOPHYSI: TELEOSTEI)

(2013) Wei-Jen Chen et al.   EVOLUTION

Less Is More in Mammalian Phylogenomics: AT-Rich Genes Minimize Tree Conflicts and Unravel the Root of Placental Mammals

(2013) Jonathan Romiguier et al.   MOLECULAR BIOLOGY AND EVOLUTION

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

STRAW: Species TRee Analysis Web server

(2013) Timothy I. Shaw et al.   NUCLEIC ACIDS RESEARCH

The Genome of the Ctenophore Mnemiopsis leidyi and Its Implications for Cell Type Evolution

(2013) J. F. Ryan et al.   SCIENCE

Addressing Gene Tree Discordance and Non-Stationarity to Resolve a Multi-Locus Phylogeny of the Flatfishes (Teleostei: Pleuronectiformes)

(2013) Ricardo Betancur-R. et al.   SYSTEMATIC BIOLOGY

Anomalous Unrooted Gene Trees

(2013) James H. Degnan   SYSTEMATIC BIOLOGY

Conserved Genes, Sampling Error, and Phylogenomic Inference

(2013) Ricardo Betancur-R. et al.   SYSTEMATIC BIOLOGY

MEGA-CC: computing core of molecular evolutionary genetics analysis program for automated and iterative data analysis

(2012) S. Kumar et al.   BIOINFORMATICS

Revisiting fitting monotone polynomials to data

(2012) Kevin Murray et al.   COMPUTATIONAL STATISTICS

EvolMarkers: a database for mining exon and intron markers for evolution, ecology and conservation studies

(2012) CHENHONG LI et al.   Molecular Ecology Resources

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

Resolution of ray-finned fish phylogeny and timing of diversification

(2012) T. J. Near et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

TreeFix: Statistically Informed Gene Tree Error Correction Using Species Trees

(2012) Yi-Chieh Wu et al.   SYSTEMATIC BIOLOGY

Evolutionary history of Otophysi (Teleostei), a major clade of the modern freshwater fishes: Pangaean origin and Mesozoic radiation

(2011) Masanori Nakatani et al.   BMC EVOLUTIONARY BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS 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

Target-enrichment strategies for next-generation sequencing

(2010) Lira Mamanova et al.   NATURE METHODS

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

Bayesian Inference of Species Trees from Multilocus Data

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

FastTree: Computing Large Minimum Evolution Trees with Profiles instead of a Distance Matrix

(2009) M. N. Price et al.   MOLECULAR BIOLOGY AND EVOLUTION

Nine exceptional radiations plus high turnover explain species diversity in jawed vertebrates

(2009) M. E. Alfaro et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

TNT, a free program for phylogenetic analysis

(2008) Pablo A. Goloboff et al.   CLADISTICS

New insights into the organization and evolution of vertebrate IRBP genes and utility of IRBP gene sequences for the phylogenetic study of the Acanthomorpha (Actinopterygii: Teleostei)

(2008) Agnès Dettaï et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION