Investigating Difficult Nodes in the Placental Mammal Tree with Expanded Taxon Sampling and Thousands of Ultraconserved Elements

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

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

The Interrelationships of Placental Mammals and the Limits of Phylogenetic Inference

(2016) James E. Tarver et al.   Genome Biology and Evolution

The phylogenomic forest of bird trees contains a hard polytomy at the root of Neoaves

(2016) Alexander Suh   ZOOLOGICA SCRIPTA

Genomic analysis reveals hidden biodiversity within colugos, the sister group to primates

(2016) V. C. Mason et al.   Science Advances

ExaML version 3: a tool for phylogenomic analyses on supercomputers

(2015) Alexey M. Kozlov et al.   BIOINFORMATICS

ASTRAL-II: coalescent-based species tree estimation with many hundreds of taxa and thousands of genes

(2015) Siavash Mirarab et al.   BIOINFORMATICS

PHYLUCE is a software package for the analysis of conserved genomic loci

(2015) Brant C. Faircloth   BIOINFORMATICS

ASTRID: Accurate Species TRees from Internode Distances

(2015) Pranjal Vachaspati et al.   BMC GENOMICS

Identifiability of the unrooted species tree topology under the coalescent model with time-reversible substitution processes, site-specific rate variation, and invariable sites

(2015) Julia Chifman et al.   JOURNAL OF THEORETICAL BIOLOGY

Applying species-tree analyses to deep phylogenetic histories: Challenges and potential suggested from a survey of empirical phylogenetic studies

(2015) Hayley C. Lanier et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

The Challenges of Resolving a Rapid, Recent Radiation: Empirical and Simulated Phylogenomics of Philippine Shrews

(2015) Thomas C. Giarla et al.   SYSTEMATIC BIOLOGY

Quartet Inference from SNP Data Under the Coalescent Model

(2014) Julia Chifman et al.   BIOINFORMATICS

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

Making the Impossible Possible: Rooting the Tree of Placental Mammals

(2013) E. C. Teeling et al.   MOLECULAR 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

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

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

How low can you go? The effects of mutation rate on the accuracy of species-tree estimation

(2013) Hayley C. Lanier et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

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

(2013) M. A. O'Leary et al.   SCIENCE

The tree shrew provides a useful alternative model for the study of influenza H1N1 virus

(2013) Zi-feng Yang et al.   Virology Journal

Cost-effective, high-throughput DNA sequencing libraries for multiplexed target capture

(2012) N. Rohland et al.   GENOME RESEARCH

SPAdes: A New Genome Assembly Algorithm and Its Applications to Single-Cell Sequencing

(2012) Anton Bankevich et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

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

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

Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales

(2012) Brant C. Faircloth et al.   SYSTEMATIC 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

Molecular phylogeny of treeshrews (Mammalia: Scandentia) and the timescale of diversification in Southeast Asia

(2011) Trina E. Roberts et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Quartet MaxCut: A fast algorithm for amalgamating quartet trees

(2011) Sagi Snir et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification

(2011) R. W. Meredith et al.   SCIENCE

Phylogenomic Analysis Resolves the Interordinal Relationships and Rapid Diversification of the Laurasiatherian Mammals

(2011) Xuming Zhou et al.   SYSTEMATIC BIOLOGY

Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough

(2011) Hervé Philippe et al.   PLOS BIOLOGY

A Molecular Phylogeny of Living Primates

(2011) Polina Perelman et al.   PLoS Genetics

DendroPy: a Python library for phylogenetic computing

(2010) J. Sukumaran et al.   BIOINFORMATICS

How Many Bootstrap Replicates Are Necessary?

(2010) Nicholas D. Pattengale et al.   JOURNAL OF COMPUTATIONAL BIOLOGY

Mammalian Evolution May not Be Strictly Bifurcating

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

Rapid radiation, ancient incomplete lineage sorting and ancient hybridization in the endemic Lake Tanganyika cichlid tribe Tropheini

(2009) Stephan Koblmüller et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Gene tree discordance, phylogenetic inference and the multispecies coalescent

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

Calculating Bootstrap Probabilities of Phylogeny Using Multilocus Sequence Data

(2008) T.-K. Seo   MOLECULAR BIOLOGY AND EVOLUTION