The OMA orthology database in 2018: retrieving evolutionary relationships among all domains of life through richer web and programmatic interfaces

Fast Genome-Wide Functional Annotation through Orthology Assignment by eggNOG-Mapper

(2017) Jaime Huerta-Cepas et al.   MOLECULAR BIOLOGY AND EVOLUTION

TnT: a set of libraries for visualizing trees and track-based annotations for the web

(2016) Miguel Pignatelli   BIOINFORMATICS

Phylo.io: Interactive Viewing and Comparison of Large Phylogenetic Trees on the Web

(2016) Oscar Robinson et al.   MOLECULAR BIOLOGY AND EVOLUTION

Genenames.org: the HGNC and VGNC resources in 2017

(2016) Bethan Yates et al.   NUCLEIC ACIDS RESEARCH

UniProt: the universal protein knowledgebase

(2016)   NUCLEIC ACIDS RESEARCH

Homoeologs: What Are They and How Do We Infer Them?

(2016) Natasha M. Glover et al.   TRENDS IN PLANT SCIENCE

The Orthology Ontology: development and applications

(2016) Jesualdo Tomás Fernández-Breis et al.   Journal of Biomedical Semantics

eggNOG 4.5: a hierarchical orthology framework with improved functional annotations for eukaryotic, prokaryotic and viral sequences

(2015) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Gene3D: expanding the utility of domain assignments

(2015) Su Datt Lam et al.   NUCLEIC ACIDS RESEARCH

Systematic humanization of yeast genes reveals conserved functions and genetic modularity

(2015) A. H. Kachroo et al.   SCIENCE

Current Methods for Automated Filtering of Multiple Sequence Alignments Frequently Worsen Single-Gene Phylogenetic Inference

(2015) Ge Tan et al.   SYSTEMATIC BIOLOGY

Big data and other challenges in the quest for orthologs

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

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

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

The OMA orthology database in 2015: function predictions, better plant support, synteny view and other improvements

(2014) Adrian M. Altenhoff et al.   NUCLEIC ACIDS RESEARCH

PLAZA 3.0: an access point for plant comparative genomics

(2014) Sebastian Proost et al.   NUCLEIC ACIDS RESEARCH

MAFFT Multiple Sequence Alignment Software Version 7: Improvements in Performance and Usability

(2013) K. Katoh et al.   MOLECULAR BIOLOGY AND EVOLUTION

Functional and evolutionary implications of gene orthology

(2013) Toni Gabaldón et al.   NATURE REVIEWS GENETICS

PhylomeDB v4: zooming into the plurality of evolutionary histories of a genome

(2013) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Inferring Hierarchical Orthologous Groups from Orthologous Gene Pairs

(2013) Adrian M. Altenhoff et al.   PLoS One

CAFA and the Open World of protein function predictions

(2013) Christophe Dessimoz et al.   TRENDS IN GENETICS

MBGD update 2013: the microbial genome database for exploring the diversity of microbial world

(2012) Ikuo Uchiyama et al.   NUCLEIC ACIDS RESEARCH

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

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

Letter to the Editor: SeqXML and OrthoXML: standards for sequence and orthology information

(2011) T. Schmitt et al.   BRIEFINGS IN BIOINFORMATICS

BioStar: An Online Question & Answer Resource for the Bioinformatics Community

(2011) Laurence D. Parnell et al.   PLoS Computational Biology

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

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

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