ArticleNucleic acids research2020
MetaPhOrs 2.0: integrative, phylogeny-based inference of orthology and paralogy across the tree of life.
Article in Nucleic acids research, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed.
- Integrated Single-Cell analysis Reveals molecular correlation of maternal-to-zygotic transition between human and pig embryo.Journal of translational medicine · 2026Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- SonicParanoid2: fast, accurate, and comprehensive orthology inference with machine learning and language models.Genome biology · 2024Article
- Review
- Probing RNA structural landscapes acrossFrontiers in microbiology · 2024Article
- Article
- Asymmetrical dose responses shape the evolutionary trade-off between antifungal resistance and nutrient use.Nature ecology & evolution · 2022Article
- Follicular Hyperstimulation Dysgenesis: New Explanation for Adverse Effects of Excessive FSH in Ovarian Stimulation.Endocrinology · 2022Article
- Transcriptome and proteome profiling reveals complex adaptations of Candida parapsilosis cells assimilating hydroxyaromatic carbon sources.PLoS genetics · 2022Article
- Genome analysis of five recently described species of the CUG-Ser clade uncovers Candida theae as a new hybrid lineage with pathogenic potential in the Candida parapsilosis species complex.DNA research : an international journal for rapid publication of reports on genes and genomes · 2022Article
- PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.Nucleic acids research · 2022Article
- Leveraging machine learning essentiality predictions and chemogenomic interactions to identify antifungal targets.Nature communications · 2021Article
- Essential shared and species-specific features of mammalian oocyte maturation-associated transcriptome changes impacting oocyte physiology.American journal of physiology. Cell physiology · 2021Article
- Nuclear RNA purification by flow cytometry to study nuclear processes in plants.STAR protocols · 2021Article
- Systematic analysis of bypass suppression of essential genes.Molecular systems biology · 2020Article
- Structure and function of the vacuolar Ccc1/VIT1 family of iron transporters and its regulation in fungi.Computational and structural biotechnology journal · 2020Review
- InFrontiers in microbiology · 2020Article
Corrections and comments
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Authors and funding
4 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Inferring homology relationships across genes in different species is a central task in comparative genomics. Therefore, a large number of resources and methods have been developed over the years. Some public databases include phylogenetic trees of homologous gene families which can be used to further differentiate homology relationships into orthology and paralogy. MetaPhOrs is a web server that integrates phylogenetic information from different sources to provide orthology and paralogy relationships based on a common phylogeny-based predictive algorithm and associated with a consistency-based confidence score. Here we describe the latest version of the web server which includes major new implementations and provides orthology and paralogy relationships derived from ∼8.2 million gene family trees-from 13 different source repositories across ∼4000 species with sequenced genomes. MetaPhOrs server is freely available, without registration, at http://orthology.phylomedb.org/.
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