simuPOP

simuPOP simulates forward-time population genetics using a Python-based scripting environment to model evolutionary processes, mating schemes, and age-structured demography.

Key Features:

• Forward-time simulation: Simulates populations over generations to model evolutionary dynamics.
• Python scripting and API: Provides a Python scripting interface with objects and functions for detailed creation, manipulation, and evolution of individuals and populations.
• Extensible architecture: Offers a flexible and extensible design to support large-scale and complex evolutionary scenarios.
• Built-in scripts: Includes built-in scripts ranging from basic population genetics models to intricate simulations under diverse evolutionary conditions.
• Customizable non-random mating schemes: Supports customizable mating schemes including partial self-mating, positive assortative mating, non-random outbreeding, and overlapping generations in age-structured populations.
• Arbitrary mating models: Enables specification and simulation of arbitrary non-random mating models.
• Batch execution: Supports execution of pre-written scripts in batch mode.
• Version-specific enhancement: Since version 0.8.5, includes enhanced capability to simulate non-random mating schemes.

Scientific Applications:

• Model evolutionary processes: Use forward-time simulations to model population-level evolutionary dynamics and demography.
• Investigate mating strategy effects: Assess genetic consequences of partial self-mating, positive assortative mating, non-random outbreeding, and overlapping generations on population structure and evolution.
• Explore complex scenarios: Study large-scale and complex evolutionary investigations, including age-structured population dynamics.

Methodology:

Forward-time simulations are implemented via a Python scripting API using objects and functions, executing built-in or user-provided scripts (including batch mode) with customizable mating schemes (e.g., partial selfing, assortative mating, non-random outbreeding, overlapping generations); enhanced non-random mating support from v0.8.5.