OrthoDB: a hierarchical catalog of animal, fungal and bacterial orthologs

Roundup 2.0: enabling comparative genomics for over 1800 genomes

(2012) T. F. DeLuca et al.   BIOINFORMATICS

QuartetS-DB: a large-scale orthology database for prokaryotes and eukaryotes inferred by evolutionary evidence

(2012) Chenggang Yu et al.   BMC BIOINFORMATICS

Orthology prediction methods: A quality assessment using curated protein families

(2011) Kalliopi Trachana et al.   BIOESSAYS

OrthoInspector: comprehensive orthology analysis and visual exploration

(2011) Benjamin Linard et al.   BMC BIOINFORMATICS

Faster Smith-Waterman database searches with inter-sequence SIMD parallelisation

(2011) Torbjørn Rognes   BMC BIOINFORMATICS

A remarkably stable TipE gene cluster: evolution of insect Para sodium channel auxiliary subunits

(2011) Jia Li et al.   BMC EVOLUTIONARY BIOLOGY

Conceptual framework and pilot study to benchmark phylogenomic databases based on reference gene trees

(2011) B. Boeckmann et al.   BRIEFINGS IN BIOINFORMATICS

A new face and new challenges for Online Mendelian Inheritance in Man (OMIM®)

(2011) Joanna Amberger et al.   HUMAN MUTATION

The Mouse Genome Database (MGD): comprehensive resource for genetics and genomics of the laboratory mouse

(2011) J. T. Eppig et al.   NUCLEIC ACIDS RESEARCH

WormBase 2012: more genomes, more data, new website

(2011) K. Yook et al.   NUCLEIC ACIDS RESEARCH

Ensembl Genomes: an integrative resource for genome-scale data from non-vertebrate species

(2011) Paul J. Kersey et al.   NUCLEIC ACIDS RESEARCH

VectorBase: improvements to a bioinformatics resource for invertebrate vector genomics

(2011) K. Megy et al.   NUCLEIC ACIDS RESEARCH

InterPro in 2011: new developments in the family and domain prediction database

(2011) S. Hunter et al.   NUCLEIC ACIDS RESEARCH

Reorganizing the protein space at the Universal Protein Resource (UniProt)

(2011)   NUCLEIC ACIDS RESEARCH

FlyBase 101 - the basics of navigating FlyBase

(2011) P. McQuilton et al.   NUCLEIC ACIDS RESEARCH

eggNOG v3.0: orthologous groups covering 1133 organisms at 41 different taxonomic ranges

(2011) S. Powell et al.   NUCLEIC ACIDS RESEARCH

The Gene Ontology: enhancements for 2011

(2011)   NUCLEIC ACIDS RESEARCH

Database resources of the National Center for Biotechnology Information

(2011) E. W. Sayers et al.   NUCLEIC ACIDS RESEARCH

Saccharomyces Genome Database: the genomics resource of budding yeast

(2011) J. M. Cherry et al.   NUCLEIC ACIDS RESEARCH

The Genome Portal of the Department of Energy Joint Genome Institute

(2011) I. V. Grigoriev et al.   NUCLEIC ACIDS RESEARCH

Ensembl 2012

(2011) P. Flicek et al.   NUCLEIC ACIDS RESEARCH

The Ecoresponsive Genome of Daphnia pulex

(2011) J. K. Colbourne et al.   SCIENCE

Creating a Buzz About Insect Genomes

(2011) G. E. Robinson et al.   SCIENCE

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

(2010) T. Junier et al.   BIOINFORMATICS

Correlating Traits of Gene Retention, Sequence Divergence, Duplicability and Essentiality in Vertebrates, Arthropods, and Fungi

(2010) Robert M. Waterhouse et al.   Genome Biology and Evolution

AphidBase: a centralized bioinformatic resource for annotation of the pea aphid genome

(2010) F. Legeai et al.   INSECT MOLECULAR BIOLOGY

Hymenoptera Genome Database: integrated community resources for insect species of the order Hymenoptera

(2010) M. C. Munoz-Torres et al.   NUCLEIC ACIDS RESEARCH

PhylomeDB v3.0: an expanding repository of genome-wide collections of trees, alignments and phylogeny-based orthology and paralogy predictions

(2010) J. Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

OrthoDB: the hierarchical catalog of eukaryotic orthologs in 2011

(2010) Robert M. Waterhouse et al.   NUCLEIC ACIDS RESEARCH

ZFIN: enhancements and updates to the zebrafish model organism database

(2010) Y. Bradford et al.   NUCLEIC ACIDS RESEARCH

OMA 2011: orthology inference among 1000 complete genomes

(2010) A. M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

FastTree 2 – Approximately Maximum-Likelihood Trees for Large Alignments

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

Genome sequences of the human body louse and its primary endosymbiont provide insights into the permanent parasitic lifestyle

(2010) E. F. Kirkness et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Pathogenomics of Culex quinquefasciatus and Meta-Analysis of Infection Responses to Diverse Pathogens

(2010) L. C. Bartholomay et al.   SCIENCE

Sequencing of Culex quinquefasciatus Establishes a Platform for Mosquito Comparative Genomics

(2010) P. Arensburger et al.   SCIENCE

Functional and Evolutionary Insights from the Genomes of Three Parasitoid Nasonia Species

(2010) J. H. Werren et al.   SCIENCE

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

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

Databases of homologous gene families for comparative genomics

(2009) Simon Penel et al.   BMC BIOINFORMATICS

Berkeley PHOG: PhyloFacts orthology group prediction web server

(2009) Ruchira S. Datta et al.   NUCLEIC ACIDS RESEARCH

BeetleBase in 2010: revisions to provide comprehensive genomic information for Tribolium castaneum

(2009) Hee Shin Kim et al.   NUCLEIC ACIDS RESEARCH

PANTHER version 7: improved phylogenetic trees, orthologs and collaboration with the Gene Ontology Consortium

(2009) Huaiyu Mi et al.   NUCLEIC ACIDS RESEARCH

SilkDB v2.0: a platform for silkworm (Bombyx mori) genome biology

(2009) Jun Duan et al.   NUCLEIC ACIDS RESEARCH

InParanoid 7: new algorithms and tools for eukaryotic orthology analysis

(2009) G. Ostlund et al.   NUCLEIC ACIDS RESEARCH

PhyloWidget: web-based visualizations for the tree of life

(2008) G. E. Jordan et al.   BIOINFORMATICS

Recent developments in the MAFFT multiple sequence alignment program

(2008) K. Katoh et al.   BRIEFINGS IN BIOINFORMATICS

EnsemblCompara GeneTrees: Complete, duplication-aware phylogenetic trees in vertebrates

(2008) A. J. Vilella et al.   GENOME RESEARCH

DEG 5.0, a database of essential genes in both prokaryotes and eukaryotes

(2008) R. Zhang et al.   NUCLEIC ACIDS RESEARCH