WGDdetector

WGDdetector detects whole genome duplication (WGD) events from genome and transcriptome annotations by estimating synonymous substitution (dS) patterns between paralogous gene pairs.

Key Features:

• Universal Application: Accepts genome and transcriptome annotations, including poorly assembled genomes, to detect WGDs across diverse organisms.
• dS-Based Methodology: Estimates dS (synonymous substitution rate) between paralogous gene pairs and analyzes dS distributions to identify duplication signals.
• Integrated Pipeline: Integrates gene family construction, dS estimation, and phasing of dS estimates into a unified computational pipeline.

Scientific Applications:

• WGD detection across taxa: Applied to plant and animal datasets including Arabidopsis thaliana, Juglans regia, Populus trichocarpa, and Xenopus laevis to detect historical WGDs.
• Comparative evolutionary inference: Uses dS distribution patterns to compare and validate inferred WGD events against previous studies.

Methodology:

Constructs gene families from input annotations, estimates dS values for paralogous pairs, and phases dS estimates to identify WGD-associated peaks using genome and transcriptome data.