doubletrouble

doubletrouble identifies duplicated genes from whole-genome protein sequences and classifies them based on their modes of duplication.

Key Features:

• Duplication mode classification: Classifies gene pairs into six duplication modes: segmental duplication (SD), tandem duplication (TD), proximal duplication (PD), retrotransposon-derived transposed duplication (rTRD), DNA transposon-derived transposed duplication (dTRD), and dispersed duplication (DD).
• Simplified classification scheme: Allows classification of duplicates into segmental duplication (SD)- and small-scale duplication (SSD)-derived gene pairs.
• Gene-level classification: Assigns each gene a unique mode of duplication.
• Substitution rate calculation: Calculates Ka and Ks substitution rates per substitution site from duplicate pairs.
• Ks distribution analysis: Finds peaks in Ks distributions with Gaussian Mixture Models (GMMs).
• Age group classification: Classifies gene pairs into age groups based on Ks peaks.
• Whole-genome duplication detection: Detects signatures of putative whole-genome duplication events.
• Visualization: Generates publication-ready figures of results.

Scientific Applications:

• Duplicated gene repertoire analysis: Enables comprehensive analysis of duplicated genes from genomic data across eukaryotic genomes.
• Evolutionary history inference: Supports inference of gene duplication history through Ks-based age group classification and whole-genome duplication detection.
• Large-scale comparative genomics: Facilitates classification of duplicated gene repertoires in hundreds of eukaryotic genomes.

Methodology:

doubletrouble identifies duplicated genes from whole-genome protein sequences, classifies them by duplication mode, calculates Ka and Ks substitution rates, finds peaks in Ks distributions with Gaussian Mixture Models (GMMs), and classifies gene pairs into age groups based on Ks peaks.