List of orthology databases

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Database Description / Scientific focus applications (Max. 2 sentences) Last updated Update frequency QFO Reference Proteomes Taxonomic range covered Number of organisms Web service available OrthoXML available
OrthoDB Comparative genomics, gene function inference, phylogenomics 2016 yearly no all domains of life and viruses >4000 Prok., 588 Euk., & >3000 vir. yes no
metaPhOrs Phylogeny-based orthologs and paralogs computed using a consistency-based algorithms and phylogenetic trees available in 12 public repositories 2015 yes all domains of life 2,714 yes no
PhylomeDB Genome-wide collection of gene evolutionary histories, and phylogeny-based orthology and paralogy prediction 2016 yes all domains of life >1000 yes yes
DIOPT Integrative ortholog prediction tool of 10 algorithms 2016 partially major model organisms 9 yes no
Ensembl Compara Evolutionary relationships among Ensembl species genes; Projection of gene names and GO annotations 2016 4-5x / year no all domains of life through 6 divisions (sets of species) 66 chordates and 240 others yes yes
eggNOG A database for phylogenetically refined Orthologous Groups and functional annotation. 2016 biennial no all domains of life (plus viruses) 1793 prokaryote proteomes, 238 eukaryotes, 352 viruses yes no
InParanoid Database of 2-species ortholog groups with inparalogs; inparalogs and seed orthologs are assigned a confidence score 2014 yes all domains of life, mostly eukaryotic 273 no yes
OMA Phylogenetic reconstruction, function prediction and ancestral genome content through different types of orthologous groups 2016 2x / year partially all domains of life >2000 yes yes
OrtholugeDB Ortholog predictions for completely sequenced bacterial and archaeal genomes, with additional assessment using Ortholuge to improve specificity 2016 1x / year no bacteria and archaea >2000 yes yes
PANTHER Evolutionary relationships among model organism genes; Inference of gene function using GO terms 2016 yearly yes all domains of life 104 yes no
PLAZA Plant comparative genomics database, focusing on dicots, monocots and green algae. More info about data types here 2014 no Viridiplantae Dicots 3.0 31, Monocots 3.0 16 no no
TreeFam Catalogue of gene families; Phylogenetic reconstruction 2012 Next update in 2015 no metazoans + model eukaryotes 109 no no
GreenPhylDB Database for comparative and functional genomics in plants. gene family clustering, manual curation and phylogenomic inference of orthologs 2014 variable no Viridiplantae 37 yes no
WORMHOLE Machine learning-based integration of 17 ortholog prediction methods. 2016 variable no major model organisms 6 yes no
FUNGIpath FUNGIpath is a web service dedicated to the exploration of fungal metabolism. More info on the database here. More info on the orthologs detection method here. 2014 variable yes http://bim.igmors.u-psud.fr/mario/ Fungi 165 yes yes for the QFO reference proteomes
Other databases: