ArticleBioinformatics (Oxford, England)2025
doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.
Article in Bioinformatics (Oxford, England), 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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Who cites it
16 citing papers in PubMed.
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- The origin of the octoploid cloudberry (Rubus chamaemorus) genome is the result of multiple and complex polyploidization events.The Journal of heredity · 2026Article
- DupyliCate: mining, classifying, and characterizing gene duplications.Scientific reports · 2026Article
- Evolutionary trajectories, early diversification, and species-specific amplification of the metazoan inhibitor of apoptosis (IAP) repertoire.Molecular biology and evolution · 2026Article
- Phylogenomic Insights into High Conservation and Lineage-Specific Expansion of the ABAPT Gene Family in Plants.International journal of molecular sciences · 2026Article
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- Comprehensive Annotation of Olfactory and Gustatory Receptor Genes and Transposable Elements Revealed Their Evolutionary Dynamics in Aphids.Molecular biology and evolution · 2025Article
- Graph-based pangenomes and pan-phenome provide a cornerstone for eggplant biology and breeding.Nature communications · 2025Article
- Characterization of a Rice GH5_11 Gene Associated with Endosperm and Seed Traits.Plants (Basel, Switzerland) · 2025Article
- SegMantX: A Novel Tool for Detecting DNA Duplications Uncovers Prevalent Duplications in Plasmids.Molecular biology and evolution · 2025Article
- Chromosome-scale genome assembly of Sauvagesia rhodoleuca (Ochnaceae) provides insights into its genome evolution and demographic history.DNA research : an international journal for rapid publication of reports on genes and genomes · 2025Article
- Assembling genomes of non-model plants: A case study with evolutionary insights from Ranunculus (Ranunculaceae).The Plant journal : for cell and molecular biology · 2025Article
- Genomes of the Caribbean reef-building corals Colpophyllia natans, Dendrogyra cylindrus, and Siderastrea siderea.G3 (Bethesda, Md.) · 2025Article
- Genomes of the Caribbean reef-building coralsbioRxiv : the preprint server for biology · 2024Article
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Authors and funding
2 authors.
Funding
Abstract
summaryGene and genome duplications are major evolutionary forces that shape the diversity and complexity of life. However, different duplication modes have distinct impacts on gene function, expression, and regulation. Existing tools for identifying and classifying duplicated genes are either outdated or not user-friendly. Here, we present doubletrouble, an R/Bioconductor package that provides a comprehensive and robust framework for analyzing duplicated genes from genomic data. doubletrouble can detect and classify gene pairs as derived from six duplication modes (segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures. We applied doubletrouble to classify the duplicated gene repertoire in 822 eukaryotic genomes, and results were made available through a user-friendly web interface. AVAILABILITY AND IMPLEMENTATION: doubletrouble is available on Bioconductor (https://bioconductor.org/packages/doubletrouble), and the source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble). doubletroubledb is available online at https://almeidasilvaf.github.io/doubletroubledb/.
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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.