SeDuS

SeDuS simulates the forward-in-time molecular evolution of segmental duplications, explicitly modeling interlocus gene conversion and crossover to study copy-number and sequence dynamics.

Key Features:

• Interlocus gene conversion: Models interlocus gene conversion with biased directionality and dependency on local sequence identity.
• Selective pressures and crossover distributions: Simulates variable selective pressures on copy-number variations and configurable crossover distributions.
• Forward-in-time simulation: Uses forward-in-time evolutionary modeling to track changes in segmental duplications over time.
• Implementation: Implemented in C++.

Scientific Applications:

• Evolution of segmental duplications: Investigates molecular mechanisms shaping segmental duplications and their contribution to genomic innovation and diversity.
• Genetic variation and adaptation: Examines how interlocus gene conversion and crossover events contribute to genetic variation and adaptation.
• Selection and copy-number dynamics: Tests hypotheses about the effects of selective pressures and crossover distributions on copy-number evolution.

Methodology:

Forward-in-time simulation modeling of segmental duplications incorporating interlocus gene conversion and crossover under specified selective pressures and crossover distributions.