WGDTree

WGDTree analyzes conditional probabilities of gene retention following whole genome duplication (WGD) events using Python-based phylogenetic reconciliation, statistical modelling, and simulation methods.

Key Features:

• Phylogenetic statistical analysis: Employs a statistical approach to assess contingency of gene retention across consecutive WGD events.
• Gene tree–species tree reconciliation: Uses gene tree–species tree reconciliation to label duplicate nodes and distinguish whole genome duplications (WGD) from single segment duplications (SSD).
• Conditional probability calculation: Calculates a statistic based on the conditional probability that a gene retained after an initial WGD will also be retained after a subsequent duplication event.
• Simulation capabilities: Simulates gene trees with embedded WGD events to test hypotheses and validate the placement of WGD events within phylogenetic frameworks.
• Python implementation: Provided as a Python package for computational analysis and integration with phylogenetic workflows.
• Simulation accuracy: Empirical testing reported high accuracy in simulation and placement of WGD events.

Scientific Applications:

• Duplicate gene retention analysis: Enables testing of mechanisms and evolutionary dynamics underlying retention of duplicate genes across successive WGD events.
• Empirical phylogenomic studies: Applied to the monocot Phalaenopsis equestris to analyze consecutive WGD events and their effects on gene retention.

Methodology:

Reconciles gene trees with species trees, integrates phylogenetic data with statistical models to compute conditional probabilities of gene retention, and simulates gene trees with embedded WGD events.