Constructing a broadly inclusive seed plant phylogeny

Disparity, diversity, and duplications in the Caryophyllales

(2017) Stephen A. Smith et al.   NEW PHYTOLOGIST

The ancestral flower of angiosperms and its early diversification

(2017) Hervé Sauquet et al.   Nature Communications

A supertree pipeline for summarizing phylogenetic and taxonomic information for millions of species

(2017) Benjamin D. Redelings et al.   PeerJ

Contentious relationships in phylogenomic studies can be driven by a handful of genes

(2017) Xing-Xing Shen et al.   Nature Ecology & Evolution

Nuclear phylogenomics of the palm subfamily Arecoideae (Arecaceae)

(2016) Jason R. Comer et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Non-equilibrium dynamics and floral trait interactions shape extant angiosperm diversity

(2016) Brian C. O'Meara et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylesystem: a git-based data store for community-curated phylogenetic estimates: Fig. 1.

(2015) Emily Jane McTavish et al.   BIOINFORMATICS

Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants

(2015) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

No substitute for real data: A cautionary note on the use of phylogenies from birth-death polytomy resolvers for downstream comparative analyses

(2015) Daniel L. Rabosky   EVOLUTION

Dissecting Molecular Evolution in the Highly Diverse Plant Clade Caryophyllales Using Transcriptome Sequencing

(2015) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

Doubtful pathways to cold tolerance in plants

(2015) Erika J. Edwards et al.   NATURE

Confluence, synnovation, and depauperons in plant diversification

(2015) Michael J. Donoghue et al.   NEW PHYTOLOGIST

Nested radiations and the pulse of angiosperm diversification: increased diversification rates often follow whole genome duplications

(2015) David C. Tank et al.   NEW PHYTOLOGIST

A metacalibrated time-tree documents the early rise of flowering plant phylogenetic diversity

(2015) Susana Magallón et al.   NEW PHYTOLOGIST

Synthesis of phylogeny and taxonomy into a comprehensive tree of life

(2015) Cody E. Hinchliff et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Orchid phylogenomics and multiple drivers of their extraordinary diversification

(2015) Thomas J. Givnish et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

The Fossil Calibration Database—A New Resource for Divergence Dating

(2015) Daniel T. Ksepka et al.   SYSTEMATIC BIOLOGY

Heterogeneous Rates of Molecular Evolution and Diversification Could Explain the Triassic Age Estimate for Angiosperms

(2015) Jeremy M. Beaulieu et al.   SYSTEMATIC BIOLOGY

PUmPER: phylogenies updated perpetually

(2014) Fernando Izquierdo-Carrasco et al.   BIOINFORMATICS

geiger v2.0: an expanded suite of methods for fitting macroevolutionary models to phylogenetic trees

(2014) Matthew W. Pennell et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

Functional distinctiveness of major plant lineages

(2014) William K. Cornwell et al.   JOURNAL OF ECOLOGY

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang 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

Some Limitations of Public Sequence Data for Phylogenetic Inference (in Plants)

(2014) Cody E. Hinchliff et al.   PLoS One

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

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

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Three keys to the radiation of angiosperms into freezing environments

(2013) Amy E. Zanne et al.   NATURE

Building the Coleoptera tree-of-life for >8000 species: composition of public DNA data and fit with Linnaean classification

(2013) LADISLAV BOCAK et al.   SYSTEMATIC ENTOMOLOGY

Rates of speciation and morphological evolution are correlated across the largest vertebrate radiation

(2013) Daniel L. Rabosky et al.   Nature Communications

Congruification: support for time scaling large phylogenetic trees

(2013) Jonathan M. Eastman et al.   Methods in Ecology and Evolution

Analyzing and Synthesizing Phylogenies Using Tree Alignment Graphs

(2013) Stephen A. Smith et al.   PLoS Computational Biology

treePL: divergence time estimation using penalized likelihood for large phylogenies

(2012) Stephen A. Smith et al.   BIOINFORMATICS

Synthesizing phylogenetic knowledge for ecological research

(2012) Jeremy M. Beaulieu et al.   ECOLOGY

The global diversity of birds in space and time

(2012) W. Jetz et al.   NATURE

Understanding angiosperm diversification using small and large phylogenetic trees

(2011) S. A. Smith et al.   AMERICAN JOURNAL OF BOTANY

Angiosperm phylogeny: 17 genes, 640 taxa

(2011) Douglas E. Soltis et al.   AMERICAN JOURNAL OF BOTANY

Performance, Accuracy, and Web Server for Evolutionary Placement of Short Sequence Reads under Maximum Likelihood

(2011) Simon A. Berger et al.   SYSTEMATIC BIOLOGY

A simple polytomy resolver for dated phylogenies

(2011) Tyler S. Kuhn et al.   Methods in Ecology and Evolution

pplacer: linear time maximum-likelihood and Bayesian phylogenetic placement of sequences onto a fixed reference tree

(2010) Frederick A Matsen et al.   BMC BIOINFORMATICS

Phylogenetic analyses reveal the shady history of C4 grasses

(2010) E. J. Edwards et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Species Selection Maintains Self-Incompatibility

(2010) E. E. Goldberg et al.   SCIENCE

The Origins of C4 Grasslands: Integrating Evolutionary and Ecosystem Science

(2010) E. J. Edwards et al.   SCIENCE

Mega-phylogeny approach for comparative biology: an alternative to supertree and supermatrix approaches

(2009) Stephen A Smith et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analysis of 73 060 taxa corroborates major eukaryotic groups

(2009) Pablo A. Goloboff et al.   CLADISTICS

Life history influences rates of climatic niche evolution in flowering plants

(2009) S. A. Smith et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Phylogenetic Signal in the Eukaryotic Tree of Life

(2008) M. J. Sanderson   SCIENCE

Rates of Molecular Evolution Are Linked to Life History in Flowering Plants

(2008) S. A. Smith et al.   SCIENCE

The PhyLoTA Browser: Processing GenBank for Molecular Phylogenetics Research

(2008) Michael J. Sanderson et al.   SYSTEMATIC BIOLOGY