wgd

wgd analyzes ancient whole-genome duplications (WGDs) by constructing Ks (synonymous substitution rate) distributions and assessing intragenomic colinearity to detect and date duplicated genomic regions.

Key Features:

• KS Distribution Construction: Constructs Ks (synonymous substitution rate) distributions to identify peaks corresponding to putative WGD events and support timing estimates.
• Intragenomic Colinearity Analysis: Provides workflows to assess intragenomic colinearity by examining gene alignment and arrangement to detect duplicated genomic regions and remnants of WGDs.
• Modeling and Visualization Tools: Includes functionalities for modeling and visualizing WGD-related data to aid interpretation of Ks distributions and colinearity results.
• Python Implementation: Implemented in Python as a computational package for WGD analyses.

Scientific Applications:

• WGD detection and dating: Detection of ancient whole-genome duplications and estimation of their timing using Ks distributions and colinearity analyses.
• Plant genome evolution: Investigation of WGD events in plant genomes to elucidate evolutionary history and lineage-specific duplication patterns.

Methodology:

Constructs Ks distributions to estimate WGD timing, analyzes intragenomic colinearity to identify duplicated regions, and applies modeling and visualization for data interpretation.