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

The origin of snakes: revealing the ecology, behavior, and evolutionary history of early snakes using genomics, phenomics, and the fossil record

(2015) Allison Y Hsiang et al.   BMC EVOLUTIONARY BIOLOGY

Pelagic neonatal fossils support viviparity and precocial life history of Cretaceous mosasaurs

(2015) Daniel J. Field et al.   PALAEONTOLOGY

kdetrees: non-parametric estimation of phylogenetic tree distributions

(2014) Grady Weyenberg et al.   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

(2014) Alex Dornburg et al.   BMC EVOLUTIONARY BIOLOGY

Global Distribution and Conservation of Evolutionary Distinctness in Birds

(2014) Walter Jetz et al.   CURRENT BIOLOGY

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

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

A comprehensive multilocus phylogeny of the Neotropical cotingas (Cotingidae, Aves) with a comparative evolutionary analysis of breeding system and plumage dimorphism and a revised phylogenetic classification

(2014) Jacob S. Berv et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

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

(2014) E. D. Jarvis et al.   SCIENCE

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

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh 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

STRAW: Species TRee Analysis Web server

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

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

The age of the crown group of passerine birds and its evolutionary significance – molecular calibrations versus the fossil record

(2013) Gerald Mayr   SYSTEMATICS AND BIODIVERSITY

The venom-gland transcriptome of the eastern diamondback rattlesnake (Crotalus adamanteus)

(2012) Darin R Rokyta et al.   BMC GENOMICS

Bayesian Phylogenetics with BEAUti and the BEAST 1.7

(2012) Alexei J. Drummond et al.   MOLECULAR BIOLOGY AND EVOLUTION

PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses

(2012) R. Lanfear et al.   MOLECULAR BIOLOGY AND EVOLUTION

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Phylogenomic datasets provide both precision and accuracy in estimating the timescale of placental mammal phylogeny

(2012) M. dos Reis et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

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

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

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

PhyDesign: an online application for profiling phylogenetic informativeness

(2011) Francesc López-Giráldez et al.   BMC EVOLUTIONARY BIOLOGY

Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)

(2011) A. Dornburg et al.   MOLECULAR BIOLOGY AND EVOLUTION

Mass extinction of birds at the Cretaceous-Paleogene (K-Pg) boundary

(2011) N. R. Longrich et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Calibrated Tree Priors for Relaxed Phylogenetics and Divergence Time Estimation

(2011) Joseph Heled et al.   SYSTEMATIC BIOLOGY

Best Practices for Justifying Fossil Calibrations

(2011) James F. Parham et al.   SYSTEMATIC BIOLOGY

Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference

(2011) Jeffrey P. Townsend et al.   SYSTEMATIC BIOLOGY

Estimating Species Trees from Unrooted Gene Trees

(2011) Liang Liu et al.   SYSTEMATIC BIOLOGY

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

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

(2010) Liang Liu et al.   BMC EVOLUTIONARY BIOLOGY

Metaves, Mirandornithes, Strisores and other novelties - a critical review of the higher-level phylogeny of neornithine birds

(2010) Gerald Mayr   JOURNAL OF ZOOLOGICAL SYSTEMATICS AND EVOLUTIONARY RESEARCH

Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships

(2010) Jeffrey P. Townsend et al.   SYSTEMATIC BIOLOGY

Accommodating Heterogenous Rates of Evolution in Molecular Divergence Dating Methods: An Example Using Intercontinental Dispersal of Plestiodon (Eumeces) Lizards

(2010) Matthew C. Brandley et al.   SYSTEMATIC BIOLOGY

An Evaluation of Phylogenetic Informativeness Profiles and the Molecular Phylogeny of Diplazontinae (Hymenoptera, Ichneumonidae)

(2010) Seraina Klopfstein et al.   SYSTEMATIC BIOLOGY

Molecular evolution of genes in avian genomes

(2010) Kiwoong Nam et al.   GENOME BIOLOGY

Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples

(2009) Michael DeGiorgio et al.   MOLECULAR BIOLOGY AND EVOLUTION

Tinamous and Moa Flock Together: Mitochondrial Genome Sequence Analysis Reveals Independent Losses of Flight among Ratites

(2009) Matthew J. Phillips et al.   SYSTEMATIC BIOLOGY

Estimating Species Phylogenies Using Coalescence Times among Sequences

(2009) Liang Liu et al.   SYSTEMATIC BIOLOGY

Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny

(2008) Matthew J. Phillips   GENE

A Phylogenomic Study of Birds Reveals Their Evolutionary History

(2008) S. J. Hackett et al.   SCIENCE

The Influence of Model Averaging on Clade Posteriors: An Example Using the Triggerfishes (Family Balistidae)

(2008) Alex Dornburg et al.   SYSTEMATIC BIOLOGY

Trees of Trees: An Approach to Comparing Multiple Alternative Phylogenies

(2008) Tom M. W. Nye   SYSTEMATIC BIOLOGY