title: OrthoDB v8: update of the hierarchical catalog of orthologs and the underlying free software.
abstract: Orthology, refining the concept of homology, is the cornerstone of evolutionary comparative studies. With the ever-increasing availability of genomic data, inference of orthology has become instrumental for generating hypotheses about gene functions crucial to many studies. This update of the OrthoDB hierarchical catalog of orthologs (http://www.orthodb.org) covers 3027 complete genomes, including the most comprehensive set of 87 arthropods, 61 vertebrates, 227 fungi and 2627 bacteria (sampling the most complete and representative genomes from over 11,000 available). In addition to the most extensive integration of functional annotations from UniProt, InterPro, GO, OMIM, model organism phenotypes and COG functional categories, OrthoDB uniquely provides evolutionary annotations including rates of ortholog sequence divergence, copy-number profiles, sibling groups and gene architectures. We re-designed the entirety of the OrthoDB website from the underlying technology to the user interface, enabling the user to specify species of interest and to select the relevant orthology level by the NCBI taxonomy. The text searches allow use of complex logic with various identifiers of genes, proteins, domains, ontologies or annotation keywords and phrases. Gene copy-number profiles can also be queried. This release comes with the freely available underlying ortholog clustering pipeline (http://www.orthodb.org/software).
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland evgenia.kriventseva@unige.ch.
authors.forename: Evgenia V
authors.initials: EV
authors.lastname: Kriventseva
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
authors.forename: Fredrik
authors.initials: F
authors.lastname: Tegenfeldt
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
authors.forename: Tom J
authors.initials: TJ
authors.lastname: Petty
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
authors.forename: Robert M
authors.initials: RM
authors.lastname: Waterhouse
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
authors.forename: Felipe A
authors.initials: FA
authors.lastname: Simão
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
authors.forename: Igor A
authors.initials: IA
authors.lastname: Pozdnyakov
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland.
authors.forename: Panagiotis
authors.initials: P
authors.lastname: Ioannidis
authors.affiliation: Department of Genetic Medicine and Development, University of Geneva Medical School, rue Michel-Servet 1, 1211 Geneva, Switzerland Swiss Institute of Bioinformatics, rue Michel-Servet 1, 1211 Geneva, Switzerland evgeny.zdobnov@unige.ch.
authors.forename: Evgeny M
authors.initials: EM
authors.lastname: Zdobnov
mesh_terms: D000465:Algorithms; D000818:Animals; D066289:Data Curation; D030541:Databases, Genetic; D056890:Eukaryota / Q000235:genetics; D019143:Evolution, Molecular; D064349:Genome, Microbial; D006801:Humans; D017385:Sequence Homology; D012984:Software