scoup

scoup simulates codon genetic sequences under varying degrees and patterns of Darwinian selection using a molecular evolutionary framework based on the fitness landscape paradigm of Sewall Wright and the mutation-selection model of Halpern and Bruno.

Key Features:

• Ornstein-Uhlenbeck fitness update: Incorporates an Ornstein-Uhlenbeck algorithm for modeling fitness landscape dynamics over evolutionary time.
• Frequency-dependent fitness updates: Supports frequency-dependent fitness landscape update techniques for population-aware evolutionary simulations.
• Stochastic fitness updates: Supports stochastic fitness landscape update techniques for modeling random environmental fluctuations.
• Genetic drift and selection interplay: Enables investigation of how the interplay between genetic drift and fitness landscape fluctuations affects inference of diversifying selection.

Scientific Applications:

• Diversifying selection inference: Facilitates investigation of how fitness landscape fluctuations and genetic drift affect the detection and interpretation of diversifying selection signals.
• Codon sequence evolution: Supports simulation-based studies of molecular evolution at the codon level under realistic selection regimes.

Methodology:

The framework implements the mutation-selection model of Halpern and Bruno built upon Sewall Wright's fitness landscape paradigm, with Ornstein-Uhlenbeck, frequency-dependent, and stochastic algorithms for fitness landscape updates during codon sequence simulation.