Conflicting signal in transcriptomic markers leads to a poorly resolved backbone phylogeny of chalcidoid wasps

Evolutionary Rate Correlation between Mitochondrial-Encoded and Mitochondria-Associated Nuclear-Encoded Proteins in Insects

(2019) Zhichao Yan et al.   MOLECULAR BIOLOGY AND EVOLUTION

The Role of Homology and Orthology in the Phylogenomic Analysis of Metazoan Gene Content

(2019) Walker Pett et al.   MOLECULAR BIOLOGY AND EVOLUTION

Quartet Sampling distinguishes lack of support from conflicting support in the green plant tree of life

(2018) James B. Pease et al.   AMERICAN JOURNAL OF BOTANY

A Comprehensive and Dated Phylogenomic Analysis of Butterflies

(2018) Marianne Espeland et al.   CURRENT BIOLOGY

Transcriptome sequence-based phylogeny of chalcidoid wasps (Hymenoptera: Chalcidoidea) reveals a history of rapid radiations, convergence, and evolutionary success

(2018) Ralph S. Peters et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Targeted Sampling and Target Capture: Assessing Phylogeographic Concordance with Genome-wide Data

(2018) Lisa N. Barrow et al.   SYSTEMATIC BIOLOGY

A new lineage of Cretaceous jewel wasps (Chalcidoidea: Diversinitidae)

(2018) Michael Haas et al.   PeerJ

Anchored phylogenomics unravels the evolution of spider flies (Diptera, Acroceridae) and reveals discordance between nucleotides and amino acids

(2018) Jessica P. Gillung et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Counties not countries: Variation in host specificity among populations of an aphid parasitoid

(2018) Keith R. Hopper et al.   Evolutionary Applications

Hybrid capture data unravel a rapid radiation of pimpliform parasitoid wasps (Hymenoptera: Ichneumonidae: Pimpliformes)

(2018) Seraina Klopfstein et al.   SYSTEMATIC ENTOMOLOGY

Pinniped Diphyly and Bat Triphyly: More Homology Errors Drive Conflicts in the Mammalian Tree

(2017) Mark S Springer et al.   JOURNAL OF HEREDITY

ModelFinder: fast model selection for accurate phylogenetic estimates

(2017) Subha Kalyaanamoorthy et al.   NATURE METHODS

Phylogenomic red flags: Homology errors and zombie lineages in the evolutionary diversification of placental mammals

(2017) John Gatesy et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

To Include or Not to Include: The Impact of Gene Filtering on Species Tree Estimation Methods

(2017) Erin K Molloy et al.   SYSTEMATIC BIOLOGY

Why Do Phylogenomic Data Sets Yield Conflicting Trees? Data Type Influences the Avian Tree of Life more than Taxon Sampling

(2017) Sushma Reddy et al.   SYSTEMATIC BIOLOGY

Taxon sampling to address an ancient rapid radiation: a supermatrix phylogeny of early brachyceran flies (Diptera)

(2017) SEUNGGWAN SHIN et al.   SYSTEMATIC ENTOMOLOGY

Evolution of lacewings and allied orders using anchored phylogenomics (Neuroptera, Megaloptera, Raphidioptera)

(2017) SHAUN L. WINTERTON et al.   SYSTEMATIC ENTOMOLOGY

On the importance of homology in the age of phylogenomics

(2017) Mark S. Springer et al.   SYSTEMATICS AND BIODIVERSITY

A Tissue-Mapped Axolotl De Novo Transcriptome Enables Identification of Limb Regeneration Factors

(2017) Donald M. Bryant et al.   Cell Reports

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

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

Terrace Aware Data Structure for Phylogenomic Inference from Supermatrices

(2016) Olga Chernomor et al.   SYSTEMATIC BIOLOGY

The Identification of the Closest Living Relative(s) of Tetrapods: Phylogenomic Lessons for Resolving Short Ancient Internodes

(2016) Iker Irisarri et al.   SYSTEMATIC BIOLOGY

AMAS: a fast tool for alignment manipulation and computing of summary statistics

(2016) Marek L. Borowiec   PeerJ

Ultrastructural Characterization of the Lower Motor System in a Mouse Model of Krabbe Disease

(2016) Valentina Cappello et al.   Scientific Reports

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

Genes with minimal phylogenetic information are problematic for coalescent analyses when gene tree estimation is biased

(2015) Zhenxiang Xi 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

Small but not ephemeral: newly discovered species of Aphelinidae and Trichogrammatidae (Insecta: Hymenoptera: Chalcidoidea) from Eocene amber

(2015) ROGER A. BURKS et al.   SYSTEMATIC ENTOMOLOGY

ASTRAL: genome-scale coalescent-based species tree estimation

(2014) S. Mirarab et al.   BIOINFORMATICS

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

(2014) Alexandros Stamatakis   BIOINFORMATICS

IQ-TREE: A Fast and Effective Stochastic Algorithm for Estimating Maximum-Likelihood Phylogenies

(2014) Lam-Tung Nguyen et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software

(2014) Evgenia V. Kriventseva et al.   NUCLEIC ACIDS RESEARCH

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

The Phylogenetic Likelihood Library

(2014) T. Flouri et al.   SYSTEMATIC BIOLOGY

Coalescent versus Concatenation Methods and the Placement of Amborella as Sister to Water Lilies

(2014) Zhenxiang Xi et al.   SYSTEMATIC BIOLOGY

Evaluating Summary Methods for Multilocus Species Tree Estimation in the Presence of Incomplete Lineage Sorting

(2014) Siavash Mirarab et al.   SYSTEMATIC BIOLOGY

A phylogenetic analysis of the megadiverse Chalcidoidea (Hymenoptera)

(2013) John M. Heraty et al.   CLADISTICS

Phylotranscriptomics: Saturated Third Codon Positions Radically Influence the Estimation of Trees Based on Next-Gen Data

(2013) Jesse W. Breinholt et al.   Genome Biology and Evolution

Decisive Data Sets in Phylogenomics: Lessons from Studies on the Phylogenetic Relationships of Primarily Wingless Insects

(2013) Emiliano Dell’Ampio 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

BaCoCa – A heuristic software tool for the parallel assessment of sequence biases in hundreds of gene and taxon partitions

(2013) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Origin of land plants using the multispecies coalescent model

(2013) Bojian Zhong et al.   TRENDS IN PLANT SCIENCE

PhyBin: binning trees by topology

(2013) Ryan R. Newton et al.   PeerJ

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

Full-length transcriptome assembly from RNA-Seq data without a reference genome

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

SignalP 4.0: discriminating signal peptides from transmembrane regions

(2011) Thomas Nordahl Petersen et al.   NATURE METHODS

A Molecular Phylogeny of the Chalcidoidea (Hymenoptera)

(2011) James B. Munro et al.   PLoS One

The Newick utilities: high-throughput phylogenetic tree processing in the UNIX shell

(2010) T. Junier et al.   BIOINFORMATICS

Fast and accurate long-read alignment with Burrows–Wheeler transform

(2010) Heng Li et al.   BIOINFORMATICS

Search and clustering orders of magnitude faster than BLAST

(2010) Robert C. Edgar   BIOINFORMATICS

Parametric and non-parametric masking of randomness in sequence alignments can be improved and leads to better resolved trees

(2010) Patrick Kück et al.   Frontiers in Zoology

FASconCAT: Convenient handling of data matrices

(2010) Patrick Kück et al.   MOLECULAR PHYLOGENETICS AND EVOLUTION

Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation

(2010) Cole Trapnell et al.   NATURE BIOTECHNOLOGY

Sources of Error Inherent in Species-Tree Estimation: Impact of Mutational and Coalescent Effects on Accuracy and Implications for Choosing among Different Methods

(2010) Huateng Huang et al.   SYSTEMATIC BIOLOGY

The Accuracy of Species Tree Estimation under Simulation: A Comparison of Methods

(2010) Adam D. Leaché et al.   SYSTEMATIC BIOLOGY

Mitochondrial bioenergetics as a major motive force of speciation

(2009) Moran Gershoni et al.   BIOESSAYS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Biodiversity: On the origin of bar codes

(2009) Nick Lane   NATURE

A Monte Carlo Approach Successfully Identifies Randomness in Multiple Sequence Alignments : A More Objective Means of Data Exclusion

(2009) Bernhard Misof et al.   SYSTEMATIC BIOLOGY