Citation Impact
Citing Papers
GHOST: Recovering Historical Signal from Heterotachously Evolved Sequence Alignments
2019
Multiple large-scale gene and genome duplications during the evolution of hexapods
2018
New Algorithms and Methods to Estimate Maximum-Likelihood Phylogenies: Assessing the Performance of PhyML 3.0
2010 Standout
Phylogenomic analyses support the monophyly of Excavata and resolve relationships among eukaryotic “supergroups”
2009 Standout
IQ-TREE 2: New Models and Efficient Methods for Phylogenetic Inference in the Genomic Era
2020 Standout
Limits of long-term selection against Neandertal introgression
2019 StandoutNobel
Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion
2015 StandoutScienceNobel
Resolution of ray-finned fish phylogeny and timing of diversification
2012 Standout
One thousand plant transcriptomes and the phylogenomics of green plants
2019 StandoutNature
Taxon sampling and the accuracy of phylogenetic analyses
2008
The performance of coalescent-based species tree estimation methods under models of missing data
2018
Genetic manipulation of Patescibacteria provides mechanistic insights into microbial dark matter and the epibiotic lifestyle
2023 StandoutNobel
From algae to angiosperms–inferring the phylogeny of green plants (Viridiplantae) from 360 plastid genomes
2014
The Effect of Ambiguous Data on Phylogenetic Estimates Obtained by Maximum Likelihood and Bayesian Inference
2009
Rapid progress on the vertebrate tree of life
2010
BMGE (Block Mapping and Gathering with Entropy): a new software for selection of phylogenetic informative regions from multiple sequence alignments
2010
A large-scale phylogeny of Amphibia including over 2800 species, and a revised classification of extant frogs, salamanders, and caecilians
2011
iGTP: A software package for large-scale gene tree parsimony analysis
2010
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
2013 Standout
OrthoFinder: phylogenetic orthology inference for comparative genomics
2019 Standout
What are the consequences of combining nuclear and mitochondrial data for phylogenetic analysis? Lessons from Plethodonsalamanders and 13 other vertebrate clades
2011
Fast and accurate methods for phylogenomic analyses
2011
SCaFoS: a tool for Selection, Concatenation and Fusion of Sequences for phylogenomics
2007
EVOLUTION OF EXTREME BODY SIZE DISPARITY IN MONITOR LIZARDS (VARANUS)
2011
Morphometrics of the Avian Small Intestine Compared with That of Nonflying Mammals: A Phylogenetic Approach
2008
Analysis of Acorus calamus Chloroplast Genome and Its Phylogenetic Implications
2005
PartitionFinder 2: New Methods for Selecting Partitioned Models of Evolution for Molecular and Morphological Phylogenetic Analyses
2016 Standout
SpedeSTEM: a rapid and accurate method for species delimitation
2010
A new genus of miniaturized and pug-nosed gecko from South America (Sphaerodactylidae: Gekkota)
2011
Accurate gene-tree reconstruction by learning gene- and species-specific substitution rates across multiple complete genomes
2007
Sexual dimorphism in primate aerobic capacity: a phylogenetic test
2010
Analysis of phylogenomic datasets reveals conflict, concordance, and gene duplications with examples from animals and plants
2015
The Colletotrichum gloeosporioides species complex
2012 Standout
Phylogenomics and the reconstruction of the tree of life
2005
CONTINUOUS AND ARRESTED MORPHOLOGICAL DIVERSIFICATION IN SISTER CLADES OF CHARACIFORM FISHES: A PHYLOMORPHOSPACE APPROACH
2008
Phylogeny and cryptic diversity in geckos (Phyllopezus; Phyllodactylidae; Gekkota) from South America’s open biomes
2011
On the Analysis of Evolutionary Change along Single Branches in a Phylogeny
2008
DID EGG-LAYING BOAS BREAK DOLLO'S LAW? PHYLOGENETIC EVIDENCE FOR REVERSAL TO OVIPARITY IN SAND BOAS (ERYX: BOIDAE)
2009
Double Digest RADseq: An Inexpensive Method for De Novo SNP Discovery and Genotyping in Model and Non-Model Species
2012 Standout
Phylogenetic relationships of phrynosomatid lizards based on nuclear and mitochondrial data, and a revised phylogeny for Sceloporus
2009
Arthropod relationships revealed by phylogenomic analysis of nuclear protein-coding sequences
2010 StandoutNature
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
2010
Phylogenetic and Trait-Based Prediction of Extinction Risk for Data-Deficient Amphibians
2019
Chloroplast genome phylogenetics: why we need independent approaches to plant molecular evolution
2005
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
2012 Standout
Estimating divergence dates and evaluating dating methods using phylogenomic and mitochondrial data in squamate reptiles
2012
Gene tree discordance, phylogenetic inference and the multispecies coalescent
2009
Dynamics of Genome Rearrangement in Bacterial Populations
2008
VERTEBRAL EVOLUTION AND THE DIVERSIFICATION OF SQUAMATE REPTILES
2011
Inferring the Evolutionary History of IncP-1 Plasmids Despite Incongruence among Backbone Gene Trees
2012
Fast Coalescent-Based Computation of Local Branch Support from Quartet Frequencies
2016
The supermatrix approach to systematics
2006
A Novel Heuristic for Local Multiple Alignment of Interspersed DNA Repeats
2009
Further use of nearly complete 28S and 18S rRNA genes to classify Ecdysozoa: 37 more arthropods and a kinorhynch
2006
Revealing pancrustacean relationships: Phylogenetic analysis of ribosomal protein genes places Collembola (springtails) in a monophyletic Hexapoda and reinforces the discrepancy between mitochondrial and nuclear DNA markers
2008
Phylogenomic Analysis Supports the Monophyly of Cryptophytes and Haptophytes and the Association of Rhizaria with Chromalveolates
2007
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
2015 StandoutNature
A standardized bacterial taxonomy based on genome phylogeny substantially revises the tree of life
2018 Standout
progressiveMauve: Multiple Genome Alignment with Gene Gain, Loss and Rearrangement
2010 Standout
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
2007
Phylogenetic relationships among iguanian lizards using alternative partitioning methods and TSHZ1: A new phylogenetic marker for reptiles
2008
Incomplete lineage sorting patterns among human, chimpanzee, and orangutan suggest recent orangutan speciation and widespread selection
2011
Dense Taxonomic EST Sampling and Its Applications for Molecular Systematics of the Coleoptera (Beetles)
2005
Seeing the Forest for the Trees: The Limitations of Phylogenies in Comparative Biology
2011
Recent Trends in Molecular Phylogenetic Analysis: Where to Next?
2010
Application of Phylogenetic Networks in Evolutionary Studies
2005 Standout
Tunicates and not cephalochordates are the closest living relatives of vertebrates
2006 StandoutNature
A Dirichlet Process Prior for Estimating Lineage-Specific Substitution Rates
2011
The prevalence of terraced treescapes in analyses of phylogenetic data sets
2018
Highly Incomplete Taxa Can Rescue Phylogenetic Analyses from the Negative Impacts of Limited Taxon Sampling
2012
Branch-length estimation bias misleads molecular dating for a vertebrate mitochondrial phylogeny
2008
Harnessing genomics for evolutionary insights
2009
Statistics and Truth in Phylogenomics
2011
Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting
2014
A COMPARATIVE METHOD FOR STUDYING ADAPTATION TO A RANDOMLY EVOLVING ENVIRONMENT
2008
Dual-strain genital herpes simplex virus type 2 (HSV-2) infection in the US, Peru, and 8 countries in sub-Saharan Africa: A nested cross-sectional viral genotyping study
2017
Phylogeny of Bacterial and Archaeal Genomes Using Conserved Genes: Supertrees and Supermatrices
2013
Bayesian Phylogenetics with BEAUti and the BEAST 1.7
2012 Standout
Arlequin suite ver 3.5: a new series of programs to perform population genetics analyses under Linux and Windows
2010 Standout
SIZE-CORRECTION AND PRINCIPAL COMPONENTS FOR INTERSPECIFIC COMPARATIVE STUDIES
2009 Standout
Impact of Missing Data on Phylogenies Inferred from Empirical Phylogenomic Data Sets
2012
The OBO Foundry: coordinated evolution of ontologies to support biomedical data integration
2007 Standout
Broad phylogenomic sampling improves resolution of the animal tree of life
2008 StandoutNature
Adaptive Radiation, Ecological Opportunity, and Evolutionary Determinism
2010
IS A NEW AND GENERAL THEORY OF MOLECULAR SYSTEMATICS EMERGING?
2008
PHYLOGENETIC ANALYSIS OF THE EVOLUTIONARY CORRELATION USING LIKELIHOOD
2009
Accuracy of phylogeny reconstruction methods combining overlapping gene data sets
2010
DnaSP 6: DNA Sequence Polymorphism Analysis of Large Data Sets
2017 Standout
A Revised Timescale for Human Evolution Based on Ancient Mitochondrial Genomes
2013 StandoutNobel
Molecular phylogeny of the scincid lizards of New Caledonia and adjacent areas: Evidence for a single origin of the endemic skinks of Tasmantis
2007
Full modeling versus summarizing gene-tree uncertainty: Method choice and species-tree accuracy
2012
Fast and Consistent Estimation of Species Trees Using Supermatrix Rooted Triples
2009
Evolutionary history of Coleoptera revealed by extensive sampling of genes and species
2018 Standout
Coalescent-based species delimitation in an integrative taxonomy
2012
Phytozome: a comparative platform for green plant genomics
2011 Standout
ModelFinder: fast model selection for accurate phylogenetic estimates
2017 Standout
An Adaptive Threshold in Mammalian Neocortical Evolution
2014
Algorithms for MDC-Based Multi-Locus Phylogeny Inference: Beyond Rooted Binary Gene Trees on Single Alleles
2011
Analysis of 81 genes from 64 plastid genomes resolves relationships in angiosperms and identifies genome-scale evolutionary patterns
2007 Standout
On the Distributions of Bootstrap Support and Posterior Distributions for a Star Tree
2008
Concatenation and Species Tree Methods Exhibit Statistically Indistinguishable Accuracy under a Range of Simulated conditions
2015
Mobile Genetic Elements Associated with Antimicrobial Resistance
2018 Standout
Phylogenetic Signal, Evolutionary Process, and Rate
2008
Phylogenomics
2005
The Cambrian Conundrum: Early Divergence and Later Ecological Success in the Early History of Animals
2011 StandoutScience
Improvement of Phylogenies after Removing Divergent and Ambiguously Aligned Blocks from Protein Sequence Alignments
2007 Standout
A comprehensive phylogeny of birds (Aves) using targeted next-generation DNA sequencing
2016 StandoutNature
Phylogenetic Supermatrix Analysis of GenBank Sequences from 2228 Papilionoid Legumes
2006
Estimating Species Trees from Unrooted Gene Trees
2011
2014
Occurrence, Classification, and Biological Function of Hydrogenases: An Overview
2007 Standout
Guided Tree Topology Proposals for Bayesian Phylogenetic Inference
2011
UFBoot2: Improving the Ultrafast Bootstrap Approximation
2017 Standout
High-Throughput Genomic Data in Systematics and Phylogenetics
2013
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
2012
To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods
2017
A Rapid Bootstrap Algorithm for the RAxML Web Servers
2008 Standout
An HSV-2 nucleoside-modified mRNA genital herpes vaccine containing glycoproteins gC, gD, and gE protects mice against HSV-1 genital lesions and latent infection
2020 StandoutNobel
GENOME TREES AND THE NATURE OF GENOME EVOLUTION
2005
High-resolution species trees without concatenation
2007
Hylid Frog Phylogeny and Sampling Strategies for Speciose Clades
2005
PHYLOGENOMICS REVEALS EXTENSIVE RETICULATE EVOLUTION INXIPHOPHORUSFISHES
2013
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
2012 Standout
Anomalous Unrooted Gene Trees
2013
Naive binning improves phylogenomic analyses
2013
Testing for Polytomies in Phylogenetic Species Trees Using Quartet Frequencies
2018
Combining Phylogenomics and Fossils in Higher-Level Squamate Reptile Phylogeny: Molecular Data Change the Placement of Fossil Taxa
2010
Testing Congruence in Phylogenomic Analysis
2008
Identifying the Basal Angiosperm Node in Chloroplast Genome Phylogenies: Sampling One's Way \nOut of the Felsenstein Zone
2005
The phylogeny of advanced snakes (Colubroidea), with discovery of a new subfamily and comparison of support methods for likelihood trees
2010
GEIGER: investigating evolutionary radiations
2007 Standout
Phylogenetic signal and linear regression on species data
2010
Branch Lengths, Support, and Congruence: Testing the Phylogenomic Approach with 20 Nuclear Loci in Snakes
2008
Testing quantitative genetic hypotheses about the evolutionary rate matrix for continuous characters
2008
Species Delimitation Using a Combined Coalescent and Information-Theoretic Approach: An Example from North American Myotis Bats
2010
Sparse Supermatrices for Phylogenetic Inference: Taxonomy, Alignment, Rogue Taxa, and the Phylogeny of Living Turtles
2009
Insect decline in the Anthropocene: Death by a thousand cuts
2021 Standout
A general species delimitation method with applications to phylogenetic placements
2013 Standout
Linking of Digital Images to Phylogenetic Data Matrices Using a Morphological Ontology
2007
A Phylogenomic Study of Birds Reveals Their Evolutionary History
2008 StandoutScience
Unifying Vertical and Nonvertical Evolution: A Stochastic ARG-based Framework
2009
Phylogenetic Inference Using Whole Genomes
2008
Bayesian Phylogenetics and Its Influence on Insect Systematics
2009
Statistical binning enables an accurate coalescent-based estimation of the avian tree
2014 Science
Asynchronous Colonization of Madagascar by the Four Endemic Clades of Primates, Tenrecs, Carnivores, and Rodents as Inferred from Nuclear Genes
2005
Taxon Sampling Affects Inferences of Macroevolutionary Processes from Phylogenetic Trees
2008
Bayesian Evolutionary Analysis with BEAST
2015
Missing Data in Phylogenetic Analysis: Reconciling Results from Simulations and Empirical Data
2011
ASTRAL: genome-scale coalescent-based species tree estimation
2014 Standout
phytools: an R package for phylogenetic comparative biology (and other things)
2011 Standout
Generation times in wild chimpanzees and gorillas suggest earlier divergence times in great ape and human evolution
2012 StandoutNobel
Animal Evolution and the Molecular Signature of Radiations Compressed in Time
2005 Science
From Trajectories to Averages: An Improved Description of the Heterogeneity of Substitution Rates Along Lineages
2012
Works of Cécile Ané being referenced
Inconsistency of Species Tree Methods under Gene Flow
2016
Using HSV-1 Genome Phylogenetics to Track Past Human Migrations
2013
Evaluating and Characterizing Ancient Whole-Genome Duplications in Plants with Gene Count Data
2016
Bayesian Estimation of Concordance among Gene Trees
2006
Detecting and Locating Whole Genome Duplications on a Phylogeny: A Probabilistic Approach
2013
Covarion Structure in Plastid Genome Evolution: A New Statistical Test
2004
Fine-Scale Phylogenetic Discordance across the House Mouse Genome
2009
Groves of Phylogenetic Trees
2009
TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD
2006
Missing the Forest for the Trees: Phylogenetic Compression and Its Implications for Inferring Complex Evolutionary Histories
2005
Bayesian Estimation of Concordance Among Gene Trees
2007
Detecting Phylogenetic Breakpoints and Discordance from Genome-Wide Alignments for Species Tree Reconstruction
2011
BUCKy: Gene tree/species tree reconciliation with Bayesian concordance analysis
2010
Analysis of comparative data with hierarchical autocorrelation
2008
Prospects for Building the Tree of Life from Large Sequence Databases
2004 Science
Comparing Two Bayesian Methods for Gene Tree/Species Tree Reconstruction: Simulations with Incomplete Lineage Sorting and Horizontal Gene Transfer
2011
Identifiability of a Markovian model of molecular evolution with gamma-distributed rates
2008
A Bayesian Perspective on a Non-parsimonious Parsimony Model
2008
TESTING FOR DIFFERENT RATES OF CONTINUOUS TRAIT EVOLUTION USING LIKELIHOOD
2006
Rphylopars: fast multivariate phylogenetic comparative methods for missing data and within‐species variation
2016