ArticleNucleic acids research2022
PhylomeDB V5: an expanding repository for genome-wide catalogues of annotated gene phylogenies.
Article in Nucleic acids research, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers, 1 of them a synthesis that pooled it.
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Who cites it
39 citing papers in PubMed, 1 synthesis or guideline pooled it, 85 citations in OpenAlex.
- Multi-ancestry whole genome sequencing analysis of lean body mass.Genome biology · 2025Pooled it
- TACTIC: A transfer learning framework to predict drug interactions in emerging pathogens.Cell reports methods · 2026Article
- Cross-species insights from ART-D to uncover evolutionarily conserved oncogenic mechanisms.Molecular systems biology · 2026Article
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- PhyloNaP: a user-friendly database of phylogeny for natural product-producing enzymes.Bioinformatics (Oxford, England) · 2026Article
- DIOPT: the DRSC Integrative Ortholog Prediction Tool, 2026 update.bioRxiv : the preprint server for biology · 2026Article
- Phylogenomics of Asgard archaea reveals a unique blend of prokaryotic-like horizontal transfer and eukaryotic-like gene duplication.Nature communications · 2026Article
- PharaohFUN: phylogenomic analysis for plant protein history and function elucidation.Molecular biology and evolution · 2026Article
- Growth promotion of milk-associated Candida zeylanoides by a cyclic lipopeptide produced by Pseudomonas.The ISME journal · 2026Article
- eggNOG v7: phylogeny-based orthology predictions and functional annotations.Nucleic acids research · 2026Article
- Quest for Orthologs in the era of Data Deluge and AI: Challenges and Innovations in Orthology Prediction and Data Integration.Journal of molecular evolution · 2025Review
- OrthoXML-Tools: A Toolkit for Manipulating OrthoXML Files for Orthology Data.Journal of molecular evolution · 2025Article
- Reconstructing Evolutionary Histories with Hierarchical Orthologous Groups.Journal of molecular evolution · 2025Review
- Linking phenotype to genotype using comprehensive genomic comparisons.Current opinion in genetics & development · 2025Review
- A chromosome-level genome assembly of the Hispid cotton rat (Sigmodon hispidus), a model for human pathogenic virus infections.BMC biology · 2025Article
- New developments for the Quest for Orthologs benchmark service.NAR genomics and bioinformatics · 2024Article
- Article
- Quest for Orthologs in the Era of Biodiversity Genomics.Genome biology and evolution · 2024Review
- DAVID Ortholog: an integrative tool to enhance functional analysis through orthologs.Bioinformatics (Oxford, England) · 2024Article
- The Catalan initiative for the Earth BioGenome Project: contributing local data to global biodiversity genomics.NAR genomics and bioinformatics · 2024Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
PhylomeDB is a unique knowledge base providing public access to minable and browsable catalogues of pre-computed genome-wide collections of annotated sequences, alignments and phylogenies (i.e. phylomes) of homologous genes, as well as to their corresponding phylogeny-based orthology and paralogy relationships. In addition, PhylomeDB trees and alignments can be downloaded for further processing to detect and date gene duplication events, infer past events of inter-species hybridization and horizontal gene transfer, as well as to uncover footprints of selection, introgression, gene conversion, or other relevant evolutionary processes in the genes and organisms of interest. Here, we describe the latest evolution of PhylomeDB (version 5). This new version includes a newly implemented web interface and several new functionalities such as optimized searching procedures, the possibility to create user-defined phylome collections, and a fully redesigned data structure. This release also represents a significant core data expansion, with the database providing access to 534 phylomes, comprising over 8 million trees, and homology relationships for genes in over 6000 species. This makes PhylomeDB the largest and most comprehensive public repository of gene phylogenies. PhylomeDB is available at http://www.phylomedb.org.
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Registered trials
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.