One of the main evolutionary processes influencing the complexity and diversity of life is the duplication of genes and genomes. Different duplication modes, however, affect gene expression, function, and regulation in different ways. The methods now in use for locating and categorizing duplicate genes are either antiquated or difficult to utilize.
In this study the authors have developed 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 transpo son-derived, and dispersed duplications), calculate substitution rates, detect signatures of putative whole-genome duplication events, and visualize results as publication-ready figures.
A user-friendly web interface was used to display the findings of the author’s application of doubletrouble to the classification of the duplicated gene repertoire in 822 eukaryotic genomes.
The source code is available in a GitHub repository (https://github.com/almeidasilvaf/doubletrouble).
Reference:
Fabricio Almeida Silva (2025) doubletrouble: an R/Bioconductor package for the identification, classification, and analysis of gene and genome duplications.Bioinformatics 41(2): btaf043