ArticleNucleic acids research2017
HieranoiDB: a database of orthologs inferred by Hieranoid.
Article in Nucleic acids research, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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14 citing papers in PubMed, 26 citations in OpenAlex.
- Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms.Molecular systems biology · 2026Article
- OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.Journal of molecular evolution · 2025Article
- EdgeHOG: a method for fine-grained ancestral gene order inference at large scale.Nature ecology & evolution · 2025Article
- Aon: a service to augment Alliance Genome Resource data with additional species.BMC research notes · 2023Article
- HGD: an integrated homologous gene database across multiple species.Nucleic acids research · 2023Article
- eggNOG 6.0: enabling comparative genomics across 12 535 organisms.Nucleic acids research · 2023Article
- KinOrtho: a method for mapping human kinase orthologs across the tree of life and illuminating understudied kinases.BMC bioinformatics · 2021Article
- Phylogenetic tree building in the genomic age.Nature reviews. Genetics · 2020Review
- Advances and Applications in the Quest for Orthologs.Molecular biology and evolution · 2019Article
- Microbial genome analysis: the COG approach.Briefings in bioinformatics · 2019Review
- iHam and pyHam: visualizing and processing hierarchical orthologous groups.Bioinformatics (Oxford, England) · 2019Article
- Tree reconciliation combined with subsampling improves large scale inference of orthologous group hierarchies.BMC bioinformatics · 2019Article
- Automated selection of homologs to track the evolutionary history of proteins.BMC bioinformatics · 2018Article
- Conservation of kinase-phosphorylation site pairings: Evidence for an evolutionarily dynamic phosphoproteome.PloS one · 2018Article
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Authors and funding
4 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
HieranoiDB (http://hieranoiDB.sbc.su.se) is a freely available on-line database for hierarchical groups of orthologs inferred by the Hieranoid algorithm. It infers orthologs at each node in a species guide tree with the InParanoid algorithm as it progresses from the leaves to the root. Here we present a database HieranoiDB with a web interface that makes it easy to search and visualize the output of Hieranoid, and to download it in various formats. Searching can be performed using protein description, identifier or sequence. In this first version, orthologs are available for the 66 Quest for Orthologs reference proteomes. The ortholog trees are shown graphically and interactively with marked speciation and duplication nodes that show the inferred evolutionary scenario, and allow for correct extraction of predicted orthologs from the Hieranoid trees.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.