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

Phylogenomics Resolves a Spider Backbone Phylogeny and Rejects a Prevailing Paradigm for Orb Web Evolution

(2014) Jason E. Bond et al.   CURRENT BIOLOGY

Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets

(2014) Rosa Fernández et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Transcriptomic Approach to Ribbon Worm Systematics (Nemertea): Resolving the Pilidiophora Problem

(2014) Sónia C. S. Andrade et al.   MOLECULAR BIOLOGY AND EVOLUTION

Novel Information Theory-Based Measures for Quantifying Incongruence among Phylogenetic Trees

(2014) Leonidas Salichos et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

(2014) E. D. Jarvis et al.   SCIENCE

Naive binning improves phylogenomic analyses

(2013) Md Shamsuzzoha Bayzid et al.   BIOINFORMATICS

Phylogenomic Analyses Elucidate the Evolutionary Relationships of Bats

(2013) Georgia Tsagkogeorga et al.   CURRENT BIOLOGY

Missing Data and Influential Sites: Choice of Sites for Phylogenetic Analysis Can Be As Important As Taxon Sampling and Model Choice

(2013) Liat Shavit Grievink et al.   Genome Biology and Evolution

Heterogeneous Models Place the Root of the Placental Mammal Phylogeny

(2013) Claire C. Morgan et al.   MOLECULAR BIOLOGY AND 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

One Thousand Two Hundred Ninety Nuclear Genes from a Genome-Wide Survey Support Lungfishes as the Sister Group of Tetrapods

(2013) Dan Liang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

(2013) Emiliano Dell’Ampio et al.   MOLECULAR BIOLOGY AND EVOLUTION

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

Inferring ancient divergences requires genes with strong phylogenetic signals

(2013) Leonidas Salichos et al.   NATURE

The African coelacanth genome provides insights into tetrapod evolution

(2013) Chris T. Amemiya et al.   NATURE

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

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

A Phylogenomic Perspective on the Radiation of Ray-Finned Fishes Based upon Targeted Sequencing of Ultraconserved Elements (UCEs)

(2013) Brant C. Faircloth et al.   PLoS One

The Placental Mammal Ancestor and the Post-K-Pg Radiation of Placentals

(2013) M. A. O'Leary et al.   SCIENCE

Conserved Genes, Sampling Error, and Phylogenomic Inference

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

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

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

(2012) Ylenia Chiari et al.   BMC BIOLOGY

Retroposon Insertion Patterns of Neoavian Birds: Strong Evidence for an Extensive Incomplete Lineage Sorting Era

(2012) A. Matzke et al.   MOLECULAR BIOLOGY AND EVOLUTION

Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets

(2012) Béatrice Roure et al.   MOLECULAR BIOLOGY AND EVOLUTION

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Highly conserved low-copy nuclear genes as effective markers for phylogenetic analyses in angiosperms

(2012) Ning Zhang et al.   NEW PHYTOLOGIST

Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling

(2012) John J. Wiens et al.   PLoS One

A Phylogenomic Approach to Vertebrate Phylogeny Supports a Turtle-Archosaur Affinity and a Possible Paraphyletic Lissamphibia

(2012) Jonathan J. Fong et al.   PLoS One

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

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

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

Difficult phylogenetic questions: more data, maybe; better methods, certainly

(2011) Hervé Philippe et al.   BMC BIOLOGY

Ultraconserved elements are novel phylogenomic markers that resolve placental mammal phylogeny when combined with species-tree analysis

(2011) J. E. McCormack et al.   GENOME RESEARCH

Pancrustacean Phylogeny in the Light of New Phylogenomic Data: Support for Remipedia as the Possible Sister Group of Hexapoda

(2011) B. M. von Reumont et al.   MOLECULAR BIOLOGY AND EVOLUTION

Multiple Genome Alignments Facilitate Development of NPCL Markers: A Case Study of Tetrapod Phylogeny Focusing on the Position of Turtles

(2011) X.-X. Shen et al.   MOLECULAR BIOLOGY AND EVOLUTION

Evolution of Modern Birds Revealed by Mitogenomics: Timing the Radiation and Origin of Major Orders

(2011) M. A. Pacheco et al.   MOLECULAR BIOLOGY AND EVOLUTION

Field guide to next-generation DNA sequencers

(2011) TRAVIS C. GLENN   Molecular Ecology Resources

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data

(2011) John J. Wiens et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

Rapid progress on the vertebrate tree of life

(2010) Robert C Thomson et al.   BMC BIOLOGY

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

A Phylogenomic Approach to Resolve the Arthropod Tree of Life

(2010) K. Meusemann et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mammalian Evolution May not Be Strictly Bifurcating

(2010) B. M. Hallstrom et al.   MOLECULAR BIOLOGY AND EVOLUTION

Did genome duplication drive the origin of teleosts? A comparative study of diversification in ray-finned fishes

(2009) Francesco Santini et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenomics Revives Traditional Views on Deep Animal Relationships

(2009) Hervé Philippe et al.   CURRENT BIOLOGY

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

IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?

(2008) Scott V. Edwards   EVOLUTION

An Improved General Amino Acid Replacement Matrix

(2008) S. Q. Le et al.   MOLECULAR BIOLOGY AND EVOLUTION

Broad phylogenomic sampling improves resolution of the animal tree of life

(2008) Casey W. Dunn et al.   NATURE

A Phylogenomic Study of Birds Reveals Their Evolutionary History

(2008) S. J. Hackett et al.   SCIENCE

Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence

(2008) Jerome C. Regier et al.   SYSTEMATIC BIOLOGY

Resolving an Ancient, Rapid Radiation in Saxifragales

(2008) Shuguang Jian et al.   SYSTEMATIC BIOLOGY

A Rapid Bootstrap Algorithm for the RAxML Web Servers

(2008) Alexandros Stamatakis et al.   SYSTEMATIC BIOLOGY