Tree2GD

Tree2GD identifies whole-genome duplication (WGD) events and characterizes associated gene duplication patterns to support phylogenomic analysis of genome evolution.

Key Features:

• Automated pipeline: Automatically performs sequence alignment, homolog recognition, gene/species tree reconciliation, Ks distribution analysis, and synteny analyses.
• WGD recovery performance: Identified all reported WGD events in benchmark datasets comprising 12 metazoan genomes and 68 angiosperms.
• Implementation: Implemented in Python and C++.

Scientific Applications:

• WGD inference and timing: Infers whole-genome duplication events and estimates their timing using Ks distributions and synteny evidence.
• Phylogenomic reconstruction: Reconstructs phylogenetic histories and gene duplication patterns to study genome evolution and the genetic basis of biodiversity.

Methodology:

Performs sequence alignment, homolog recognition, gene/species tree reconciliation, Ks distribution analysis (synonymous substitution rates), and synteny analyses.