A New Orthology Assessment Method for Phylogenomic Data: Unrooted Phylogenetic Orthology

Error, signal, and the placement of Ctenophora sister to all other animals

(2015) Nathan V. Whelan et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Phylogenomic resolution of scorpions reveals multilevel discordance with morphological phylogenetic signal

(2015) P. P. Sharma et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Integrating Sequence Evolution into Probabilistic Orthology Analysis

(2015) Ikram Ullah et al.   SYSTEMATIC BIOLOGY

It's more than stamp collecting: how genome sequencing can unify biological research

(2015) Stephen Richards   TRENDS IN GENETICS

Nuclear genomic signals of the ‘microturbellarian’ roots of platyhelminth evolutionary innovation

(2015) Christopher E Laumer et al.   eLife

Big data and other challenges in the quest for orthologs

(2014) E. L. L. Sonnhammer et al.   BIOINFORMATICS

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

Phylogenomic Analysis of Spiders Reveals Nonmonophyly of Orb Weavers

(2014) Rosa Fernández et al.   CURRENT BIOLOGY

Phylogenomics Resolves a Spider Backbone Phylogeny and Rejects a Prevailing Paradigm for Orb Web Evolution

(2014) Jason E. Bond et al.   CURRENT BIOLOGY

Shifting habitats, morphology, and selective pressures: Developmental polyphenism in an adaptive radiation of Hawaiian spiders

(2014) Michael S. Brewer et al.   EVOLUTION

New sequencing technologies, the development of genomics tools, and their applications in evolutionary arachnology

(2014) Michael S. Brewer et al.   JOURNAL OF ARACHNOLOGY

Comparative Transcriptomics of Maturity-Associated Color Change in Hawaiian Spiders

(2014) K. M. Yim et al.   JOURNAL OF HEREDITY

Evaluating Topological Conflict in Centipede Phylogeny Using Transcriptomic Data Sets

(2014) Rosa Fernández et al.   MOLECULAR BIOLOGY AND EVOLUTION

A Transcriptomic Approach to Ribbon Worm Systematics (Nemertea): Resolving the Pilidiophora Problem

(2014) Sónia C. S. Andrade et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phylogenomic Interrogation of Arachnida Reveals Systemic Conflicts in Phylogenetic Signal

(2014) Prashant P. Sharma et al.   MOLECULAR BIOLOGY AND EVOLUTION

Orthology Inference in Nonmodel Organisms Using Transcriptomes and Low-Coverage Genomes: Improving Accuracy and Matrix Occupancy for Phylogenomics

(2014) Ya Yang et al.   MOLECULAR BIOLOGY AND EVOLUTION

OrthoMaM v8: A Database of Orthologous Exons and Coding Sequences for Comparative Genomics in Mammals

(2014) E. J. P. Douzery et al.   MOLECULAR BIOLOGY AND EVOLUTION

InParanoid 8: orthology analysis between 273 proteomes, mostly eukaryotic

(2014) Erik L.L. Sonnhammer et al.   NUCLEIC ACIDS RESEARCH

Phylogenomics resolves the timing and pattern of insect evolution

(2014) B. Misof et al.   SCIENCE

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

(2014) E. D. Jarvis et al.   SCIENCE

High-Throughput Genomic Data in Systematics and Phylogenetics

(2013) Emily Moriarty Lemmon et al.   Annual Review of Ecology Evolution and Systematics

Systematics, Phylogeny, and Evolution of Orb-Weaving Spiders

(2013) Gustavo Hormiga et al.   Annual Review of Entomology

Agalma: an automated phylogenomics workflow

(2013) Casey W Dunn et al.   BMC BIOINFORMATICS

De novo characterization of the gene-rich transcriptomes of two color-polymorphic spiders, Theridion grallator and T. californicum (Araneae: Theridiidae), with special reference to pigment genes

(2013) Peter JP Croucher et al.   BMC GENOMICS

PhyloTreePruner: A Phylogenetic Tree-Based Approach for selection of Orthologous sequences for phylogenomics

(2013) Kevin M. Kocot et al.   Evolutionary Bioinformatics

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

SuperQ: Computing Supernetworks from Quartets

(2013) Stefan Grunewald et al.   IEEE-ACM Transactions on Computational Biology and Bioinformatics

Analysis of transcriptomes of three orb-web spider species reveals gene profiles involved in silk and toxin

(2013) Ying-Jun Zhao et al.   Insect Science

The Global Invertebrate Genomics Alliance (GIGA): Developing Community Resources to Study Diverse Invertebrate Genomes

(2013)   JOURNAL OF HEREDITY

The i5K Initiative: Advancing Arthropod Genomics for Knowledge, Human Health, Agriculture, and the Environment

(2013)   JOURNAL OF HEREDITY

Pheromone Evolution, Reproductive Genes, and Comparative Transcriptomics in Mediterranean Earthworms (Annelida, Oligochaeta, Hormogastridae)

(2013) Marta Novo 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

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

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

The PhyloFacts FAT-CAT web server: ortholog identification and function prediction using fast approximate tree classification

(2013) Cyrus Afrasiabi et al.   NUCLEIC ACIDS RESEARCH

Targeted Enrichment: Maximizing Orthologous Gene Comparisons across Deep Evolutionary Time

(2013) Shannon M. Hedtke et al.   PLoS One

The Venom Gland Transcriptome of Latrodectus tredecimguttatus Revealed by Deep Sequencing and cDNA Library Analysis

(2013) Quanze He et al.   PLoS One

Can RNA-Seq Resolve the Rapid Radiation of Advanced Moths and Butterflies (Hexapoda: Lepidoptera: Apoditrysia)? An Exploratory Study

(2013) Adam L. Bazinet et al.   PLoS One

When Outgroups Fail; Phylogenomics of Rooting the Emerging Pathogen, Coxiella burnetii

(2013) Talima Pearson et al.   SYSTEMATIC BIOLOGY

CD-HIT: accelerated for clustering the next-generation sequencing data

(2012) Limin Fu et al.   BIOINFORMATICS

Gone with the plate: the opening of the Western Mediterranean basin drove the diversification of ground-dweller spiders

(2012) Leticia Bidegaray-Batista et al.   BMC EVOLUTIONARY BIOLOGY

Orthologous genes identified by transcriptome sequencing in the spider genus Stegodyphus

(2012) Tiina M Mattila et al.   BMC GENOMICS

Genome-scale coestimation of species and gene trees

(2012) B. Boussau et al.   GENOME RESEARCH

Phylotranscriptomics to Bring the Understudied into the Fold: Monophyletic Ostracoda, Fossil Placement, and Pancrustacean Phylogeny

(2012) Todd H. Oakley et al.   MOLECULAR BIOLOGY AND EVOLUTION

A computational pipeline to discover highly phylogenetically informative genes in sequenced genomes: application to Saccharomyces cerevisiae natural strains

(2012) Matteo Ramazzotti et al.   NUCLEIC ACIDS RESEARCH

Anchored Hybrid Enrichment for Massively High-Throughput Phylogenomics

(2012) Alan R. Lemmon et al.   SYSTEMATIC BIOLOGY

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

Computational methods for Gene Orthology inference

(2011) D. M. Kristensen et al.   BRIEFINGS IN BIOINFORMATICS

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

Statistics and Truth in Phylogenomics

(2011) S. Kumar et al.   MOLECULAR BIOLOGY AND EVOLUTION

Resolving the evolutionary relationships of molluscs with phylogenomic tools

(2011) Stephen A. Smith et al.   NATURE

Phylogenomics reveals deep molluscan relationships

(2011) Kevin M. Kocot et al.   NATURE

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

(2011) Manfred G Grabherr et al.   NATURE BIOTECHNOLOGY

QuartetS: a fast and accurate algorithm for large-scale orthology detection

(2011) Chenggang Yu et al.   NUCLEIC ACIDS RESEARCH

TreeKO: a duplication-aware algorithm for the comparison of phylogenetic trees

(2011) Marina Marcet-Houben et al.   NUCLEIC ACIDS RESEARCH

Evaluating Ortholog Prediction Algorithms in a Yeast Model Clade

(2011) Leonidas Salichos et al.   PLoS One

MicroRNAs and phylogenomics resolve the relationships of Tardigrada and suggest that velvet worms are the sister group of Arthropoda

(2011) L. I. Campbell et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Tangled in a sparse spider web: single origin of orb weavers and their spinning work unravelled by denser taxonomic sampling

(2011) D. Dimitrov et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Improving animal phylogenies with genomic data

(2011) Maximilian J. Telford et al.   TRENDS IN GENETICS

phangorn: phylogenetic analysis in R

(2010) Klaus Peter Schliep   BIOINFORMATICS

ETE: a python Environment for Tree Exploration

(2010) Jaime Huerta-Cepas et al.   BMC BIOINFORMATICS

Morphology to the rescue: molecular data and the signal of morphological characters in combined phylogenetic analyses-a case study from mysmenid spiders (Araneae, Mysmenidae), with comments on the evolution of web architecture

(2010) Lara Lopardo et al.   CLADISTICS

The utility of ITS2 in spider phylogenetics: notes on prior work and an example from Anelosimus

(2010) Ingi Agnarsson   JOURNAL OF ARACHNOLOGY

Biases in Illumina transcriptome sequencing caused by random hexamer priming

(2010) Kasper D. Hansen et al.   NUCLEIC ACIDS RESEARCH

TranslatorX: multiple alignment of nucleotide sequences guided by amino acid translations

(2010) Federico Abascal et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

(2010) Morgan N. Price et al.   PLoS One

Characterizing phylogenetically decisive taxon coverage

(2009) Mike Steel et al.   APPLIED MATHEMATICS LETTERS

ShortRead: a bioconductor package for input, quality assessment and exploration of high-throughput sequence data

(2009) M. Morgan et al.   BIOINFORMATICS

trimAl: a tool for automated alignment trimming in large-scale phylogenetic analyses

(2009) S. Capella-Gutierrez et al.   BIOINFORMATICS

Biopython: freely available Python tools for computational molecular biology and bioinformatics

(2009) P. J. A. Cock et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Reconstructing web evolution and spider diversification in the molecular era

(2009) T. A. Blackledge et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Assessing the root of bilaterian animals with scalable phylogenomic methods

(2009) A. Hejnol et al.   PROCEEDINGS OF THE ROYAL SOCIETY B-BIOLOGICAL SCIENCES

Probabilistic Orthology Analysis

(2009) Bengt Sennblad et al.   SYSTEMATIC BIOLOGY

Phylogenetic and Functional Assessment of Orthologs Inference Projects and Methods

(2009) Adrian M. Altenhoff et al.   PLoS Computational Biology

Algorithm of OMA for large-scale orthology inference

(2008) Alexander CJ Roth et al.   BMC BIOINFORMATICS

A General Definition and Nomenclature for Alternative Splicing Events

(2008) Michael Sammeth et al.   PLoS Computational Biology

Large-scale assignment of orthology: back to phylogenetics?

(2008) Toni Gabaldón   GENOME BIOLOGY