doubletrouble

doubletrouble provides a comprehensive framework for identifying, classifying, and analyzing gene and genome duplications from genomic data in R/Bioconductor.

Key Features:

• Duplication mode detection: Detects and classifies gene pairs as derived from six duplication modes including segmental, tandem, proximal, retrotransposon-derived, DNA transposon-derived, and dispersed duplications.
• Substitution rate calculation: Calculates substitution rates for duplicated gene pairs.
• Whole-genome duplication detection: Detects signatures of putative whole-genome duplication events.
• Visualization: Generates publication-ready figures of results.

Scientific Applications:

• Duplicated gene repertoire classification: Classifies duplicated gene repertoires across eukaryotic genomes, as demonstrated in 822 eukaryotic genomes.
• Evolutionary consequence analysis: Enables study of the evolutionary consequences of gene and genome duplications on gene function, expression, and regulation.

Methodology:

The package analyzes duplicated genes from genomic data using methods for duplication mode classification, substitution rate calculation, and whole-genome duplication signature detection.