Related references
Note: Only part of the references are listed.ASTRAL: genome-scale coalescent-based species tree estimation
S. Mirarab et al.
BIOINFORMATICS (2014)
Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects
Emiliano Dell'Ampio et al.
MOLECULAR BIOLOGY AND EVOLUTION (2014)
Target Capture and Massively Parallel Sequencing of Ultraconserved Elements for Comparative Studies at Shallow Evolutionary Time Scales
Brian Tilston Smith et al.
SYSTEMATIC BIOLOGY (2014)
Mitochondrial Phylogenomics of Early Land Plants: Mitigating the Effects of Saturation, Compositional Heterogeneity, and Codon-Usage Bias
Yang Liu et al.
SYSTEMATIC BIOLOGY (2014)
High-Throughput Genomic Data in Systematics and Phylogenetics
Emily Moriarty Lemmon et al.
ANNUAL REVIEW OF ECOLOGY, EVOLUTION, AND SYSTEMATICS, VOL 44 (2013)
Phylogeny and biogeography of a shallow water fish clade (Teleostei: Blenniiformes)
Hsiu-Chin Lin et al.
BMC EVOLUTIONARY BIOLOGY (2013)
A phylogeny and revised classification of Squamata, including 4161 species of lizards and snakes
R. Alexander Pyron et al.
BMC EVOLUTIONARY BIOLOGY (2013)
MICROEVOLUTIONARY PROCESSES GENERATE PHYLOGENOMIC DISCORDANCE AT ANCIENT DIVERGENCES
Jeffrey C. Oliver
EVOLUTION (2013)
Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data
Jesse W. Breinholt et al.
GENOME BIOLOGY AND EVOLUTION (2013)
Phylogenetic Models of Molecular Evolution: Next-Generation Data, Fit, and Performance
David Posada
JOURNAL OF MOLECULAR EVOLUTION (2013)
Genome-wide RAD sequence data provide unprecedented resolution of species boundaries and relationships in the Lake Victoria cichlid adaptive radiation
Catherine E. Wagner et al.
MOLECULAR ECOLOGY (2013)
A Phylogeny of Birds Based on Over 1,500 Loci Collected by Target Enrichment and High-Throughput Sequencing
John E. McCormack et al.
PLOS ONE (2013)
The Impact of Paralogy on Phylogenomic Studies - A Case Study on Annelid Relationships
Torsten H. Struck
PLOS ONE (2013)
Targeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time
Shannon M. Hedtke et al.
PLOS ONE (2013)
Phylogeny and tempo of diversification in the superradiation of spiny-rayed fishes
Thomas J. Near et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2013)
Molecular and fossil evidence place the origin of cichlid fishes long after Gondwanan rifting
Matt Friedman et al.
PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2013)
Phylogenomic analyses support the position of turtles as the sister group of birds and crocodiles (Archosauria)
Ylenia Chiari et al.
BMC BIOLOGY (2012)
Assembling the Squamate Tree of Life: Perspectives from the Phenotype and the Fossil Record
Jacques A. Gauthier et al.
BULLETIN OF THE PEABODY MUSEUM OF NATURAL HISTORY (2012)
Relaxed Clocks and Inferences of Heterogeneous Patterns of Nucleotide Substitution and Divergence Time Estimates across Whales and Dolphins (Mammalia: Cetacea)
Alex Dornburg et al.
MOLECULAR BIOLOGY AND EVOLUTION (2012)
PartitionFinder: Combined Selection of Partitioning Schemes and Substitution Models for Phylogenetic Analyses
Robert Lanfear et al.
MOLECULAR BIOLOGY AND EVOLUTION (2012)
Resolution of ray-finned fish phylogeny and timing of diversification
Thomas J. Near et al.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA (2012)
Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics
Alan R. Lemmon et al.
SYSTEMATIC BIOLOGY (2012)
The Evolution of Pharyngognathy: A Phylogenetic and Functional Appraisal of the Pharyngeal Jaw Key Innovation in Labroid Fishes and Beyond
Peter C. Wainwright et al.
SYSTEMATIC BIOLOGY (2012)
MrBayes 3.2: Efficient Bayesian Phylogenetic Inference and Model Choice Across a Large Model Space
Fredrik Ronquist et al.
SYSTEMATIC BIOLOGY (2012)
Ultraconserved Elements Anchor Thousands of Genetic Markers Spanning Multiple Evolutionary Timescales
Brant C. Faircloth et al.
SYSTEMATIC BIOLOGY (2012)
ProtTest 3: fast selection of best-fit models of protein evolution
Diego Darriba et al.
BIOINFORMATICS (2011)
Exome sequencing as a tool for Mendelian disease gene discovery
Michael J. Bamshad et al.
NATURE REVIEWS GENETICS (2011)
Impacts of the Cretaceous Terrestrial Revolution and KPg Extinction on Mammal Diversification
Robert W. Meredith et al.
SCIENCE (2011)
Resolving Difficult Phylogenetic Questions: Why More Sequences Are Not Enough
Herve Philippe et al.
PLOS BIOLOGY (2011)
A maximum pseudo-likelihood approach for estimating species trees under the coalescent model
Liang Liu et al.
BMC EVOLUTIONARY BIOLOGY (2010)
Target-enrichment strategies for next-generation sequencing
Lira Mamanova et al.
NATURE METHODS (2010)
Optimal Selection of Gene and Ingroup Taxon Sampling for Resolving Phylogenetic Relationships
Jeffrey P. Townsend et al.
SYSTEMATIC BIOLOGY (2010)
Assessing what is needed to resolve a molecular phylogeny: simulations and empirical data from emydid turtles
Phillip Q. Spinks et al.
BMC EVOLUTIONARY BIOLOGY (2009)
HaMStR: Profile hidden markov model based search for orthologs in ESTs
Ingo Ebersberger et al.
BMC EVOLUTIONARY BIOLOGY (2009)
RNF213, a new nuclear marker for acanthomorph phylogeny
Blaise Li et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2009)
Interrelationships of Atherinomorpha (medakas, flyingfishes, killifishes, silversides, and their relatives): The first evidence based on whole mitogenome sequences
Davin H. E. Setiamarga et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2008)
Improvement of molecular phylogenetic inference and the phylogeny of Bilateria
Nicolas Lartillot et al.
PHILOSOPHICAL TRANSACTIONS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES (2008)
A phylogenomic study of birds reveals their evolutionary history
Shannon J. Hackett et al.
SCIENCE (2008)
The Influence of Model Averaging on Clade Posteriors: An Example Using the Triggerfishes (Family Balistidae)
Alex Dornburg et al.
SYSTEMATIC BIOLOGY (2008)
Resolving Arthropod Phylogeny: Exploring Phylogenetic Signal within 41 kb of Protein-Coding Nuclear Gene Sequence
Jerome C. Regier et al.
SYSTEMATIC BIOLOGY (2008)
Resolving an ancient, rapid radiation in Saxifragales
Shuguang Jian et al.
SYSTEMATIC BIOLOGY (2008)
AWTY (are we there yet?): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics
Johan A. A. Nylander et al.
BIOINFORMATICS (2008)
Deciphering ancient rapid radiations
James B. Whitfield et al.
TRENDS IN ECOLOGY & EVOLUTION (2007)
A practical approach to phylogenomics: the phylogeny of ray-finned fish (Actinopterygii) as a case study
Chenhong Li et al.
BMC EVOLUTIONARY BIOLOGY (2007)
Independent evolution of the specialized pharyngeal jaw apparatus in cichlid and labrid fishes
Kohji Mabuchi et al.
BMC EVOLUTIONARY BIOLOGY (2007)
Lack of resolution in the animal phylogeny: Closely spaced cladogeneses or undetected systematic errors?
Denis Baurain et al.
MOLECULAR BIOLOGY AND EVOLUTION (2007)
Detecting and overcoming systematic errors in genome-scale phylogenies
Naiara Rodriguez-Ezpeleta et al.
SYSTEMATIC BIOLOGY (2007)
A Bayesian compound stochastic process for modeling nonstationary and nonhomogeneous sequence evolution
Samuel Blanquart et al.
MOLECULAR BIOLOGY AND EVOLUTION (2006)
RAxML-VI-HPC: Maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models
Alexandros Stamatakis
BIOINFORMATICS (2006)
Phylogenomics: the beginning of incongruence?
O Jeffroy et al.
TRENDS IN GENETICS (2006)
Animal evolution and the molecular signature of radiations compressed in time
A Rokas et al.
SCIENCE (2005)
How much data are needed to resolve a difficult phylogeny? Case study in Lamiales
AH Wortley et al.
SYSTEMATIC BIOLOGY (2005)
The phylogenetic position of toadfishes (order Batrachoidiformes) in the higher ray-finned fish as inferred from partitioned Bayesian analysis of 102 whole mitochondrial genome sequences
M Miya et al.
BIOLOGICAL JOURNAL OF THE LINNEAN SOCIETY (2005)
More genes or more taxa? The relative contribution of gene number and taxon number to phylogenetic accuracy
A Rokas et al.
MOLECULAR BIOLOGY AND EVOLUTION (2005)
Phylogenomics and the reconstruction of the tree of life
F Delsuc et al.
NATURE REVIEWS GENETICS (2005)
MUSCLE: multiple sequence alignment with high accuracy and high throughput
RC Edgar
NUCLEIC ACIDS RESEARCH (2004)
Polyphyly of the mail-cheeked fishes (Teleostei: Scorpaeniformes):: evidence from mitochondrial and nuclear sequence data
WL Smith et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2004)
Phylogeny and biogeography of cichlid fishes (Teleostei: Perciformes: Cichlidae)
JS Sparks et al.
CLADISTICS (2004)
A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process
N Lartillot et al.
MOLECULAR BIOLOGY AND EVOLUTION (2004)
Fugu genome analysis provides evidence for a whole-genome duplication early during the evolution of ray-finned fishes
A Christoffels et al.
MOLECULAR BIOLOGY AND EVOLUTION (2004)
Genome-scale approaches to resolving incongruence in molecular phylogenies
A Rokas et al.
NATURE (2003)
OrthoMCL: Identification of ortholog groups for eukaryotic genomes
L Li et al.
GENOME RESEARCH (2003)
Repeatability of clades as a criterion of reliability: a case study for molecular phylogeny of Acanthomorpha (Teleostei) with larger number of taxa
WJ Chen et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)
Major patterns of higher teleostean phylogenies: a new perspective based on 100 complete mitochondrial DNA sequences
M Miya et al.
MOLECULAR PHYLOGENETICS AND EVOLUTION (2003)
Increased taxon sampling greatly reduces phylogenetic error
DJ Zwickl et al.
SYSTEMATIC BIOLOGY (2002)
An efficient algorithm for large-scale detection of protein families
AJ Enright et al.
NUCLEIC ACIDS RESEARCH (2002)