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orthology_databases [2023/11/15 15:51]
Marina Marcet Houben
orthology_databases [2023/11/24 12:57] (current)
Diego Fuentes Updated Metaphors
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 | [[http://​hieranoidb.sbc.su.se/​|HieranoiDB]] | Database of ortholog trees inferred by Hieranoid; speciation and duplication nodes are marked; inparalogs are assigned a confidence score | 2016 |     | yes | all domains of life  | 66 | no | yes | | [[http://​hieranoidb.sbc.su.se/​|HieranoiDB]] | Database of ortholog trees inferred by Hieranoid; speciation and duplication nodes are marked; inparalogs are assigned a confidence score | 2016 |     | yes | all domains of life  | 66 | no | yes |
 | [[http://​inparanoidb.sbc.su.se/​|InParanoiDB]] | Database of 2-species full-length protein and domain ortholog groups with inparalogs; inparalogs and seed orthologs are assigned a confidence score | 2023 |     | yes | all domains of life  | [[https://​inparanoidb9.sbc.su.se/​statistics/​|640]] ​ | no | yes | | [[http://​inparanoidb.sbc.su.se/​|InParanoiDB]] | Database of 2-species full-length protein and domain ortholog groups with inparalogs; inparalogs and seed orthologs are assigned a confidence score | 2023 |     | yes | all domains of life  | [[https://​inparanoidb9.sbc.su.se/​statistics/​|640]] ​ | no | yes |
-| [[http://betaorthology.phylomedb.org/​|metaPhOrs]] | Phylogeny-based orthologs and paralogs computed using a consistency-based algorithms and phylogenetic trees available in 12 public repositories | 2020 | | yes | all domains of life | 2,714 | yes | no |+| [[http://orthology.phylomedb.org/​|metaPhOrs]] | Phylogeny-based orthologs and paralogs computed using a consistency-based algorithms and phylogenetic trees available in 12 public repositories | 2021 | | yes | all domains of life | 6,384 | yes | no |
 | [[http://​omabrowser.org/​|OMA]] | [[http://​omabrowser.org/​oma/​about|Phylogenetic reconstruction,​ function prediction and ancestral genome content through different types of orthologous groups]] | [[https://​omabrowser.org/​static/​image/​history.png|2023]] | 2x / year  | partially | all domains of life | >2500 | [[http://​omabrowser.org/​api/​docs|yes]] ​ | yes | | [[http://​omabrowser.org/​|OMA]] | [[http://​omabrowser.org/​oma/​about|Phylogenetic reconstruction,​ function prediction and ancestral genome content through different types of orthologous groups]] | [[https://​omabrowser.org/​static/​image/​history.png|2023]] | 2x / year  | partially | all domains of life | >2500 | [[http://​omabrowser.org/​api/​docs|yes]] ​ | yes |
 | [[http://​orthodb.org/​|OrthoDB]] | Comparative genomics, gene function inference, phylogenomics | [[http://​www.ncbi.nlm.nih.gov/​pubmed?​cmd=Search&​term=27899580|2016]] | yearly ​ | no | all domains of life and viruses | >4000 Prok., 588 Euk., & >3000 vir. | [[http://​www.orthodb.org/?​page=api|yes]] ​ | no | | [[http://​orthodb.org/​|OrthoDB]] | Comparative genomics, gene function inference, phylogenomics | [[http://​www.ncbi.nlm.nih.gov/​pubmed?​cmd=Search&​term=27899580|2016]] | yearly ​ | no | all domains of life and viruses | >4000 Prok., 588 Euk., & >3000 vir. | [[http://​www.orthodb.org/?​page=api|yes]] ​ | no |