PhyInformR: phylogenetic experimental design and phylogenomic data exploration in R

Utility of characters evolving at diverse rates of evolution to resolve quartet trees with unequal branch lengths: analytical predictions of long-branch effects

(2015) Zhuo Su et al.   BMC EVOLUTIONARY BIOLOGY

Phylogenetic analysis of molecular and morphological data highlights uncertainty in the relationships of fossil and living species of Elopomorpha (Actinopterygii: Teleostei)

(2015) Alex Dornburg et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Genome-wide ultraconserved elements exhibit higher phylogenetic informativeness than traditional gene markers in percomorph fishes

(2015) Princess S. Gilbert et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2015) Richard O. Prum et al.   NATURE

Solving the ecological puzzle of mycorrhizal associations using data from annotated collections and environmental samples - an example of saddle fungi

(2015) Jonathan Hwang et al.   Environmental Microbiology Reports

Phylogenetic informativeness reconciles ray-finned fish molecular divergence times

(2014) Alex Dornburg et al.   BMC EVOLUTIONARY BIOLOGY

The impact of shifts in marine biodiversity hotspots on patterns of range evolution: Evidence from the Holocentridae (squirrelfishes and soldierfishes)

(2014) Alex Dornburg et al.   EVOLUTION

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

(2014) E. D. Jarvis et al.   SCIENCE

BOOM AND BUST: ANCIENT AND RECENT DIVERSIFICATION IN BICHIRS (POLYPTERIDAE: ACTINOPTERYGII), A RELICTUAL LINEAGE OF RAY-FINNED FISHES

(2013) Thomas J. Near 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

Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes

(2013) T. J. Near 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

PhyDesign: an online application for profiling phylogenetic informativeness

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

Taxon Sampling and the Optimal Rates of Evolution for Phylogenetic Inference

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

phytools: an R package for phylogenetic comparative biology (and other things)

(2011) Liam J. Revell   Methods in Ecology and Evolution

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

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

(2010) Jeffrey P. Townsend 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

Phylogenies reveal new interpretation of speciation and the Red Queen

(2009) Chris Venditti et al.   NATURE

Phylogenetic Inference Using Whole Genomes

(2008) Bruce Rannala et al.   Annual Review of Genomics and Human Genetics

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

(2008) Alex Dornburg et al.   SYSTEMATIC BIOLOGY