Genetic Drift Simulator

Overview

Genetic Drift Simulator is a Python-based simulation of genetic drift based on the Wright-Fisher model. This tool allows users to visualize how allele frequencies change over time due to random sampling in a finite population.

Project Status

Completed / Open to updates: This repository provides a fully functional GUI for exploring population genetics. It was developed as a visualization tool to illustrate stochastic processes in evolutionary biology, specifically how random sampling error affects allele frequencies in small populations.

Stochastic Modeling Approach

As a tool designed for educational visualization, this simulator prioritizes clarity and real-time interaction. By using NumPy for vectorized sampling and Matplotlib for dynamic plotting, it demonstrates how stochastic processes can lead to the fixation or loss of alleles in a population without the need for complex agent-based modeling. Every algorithmic choice was made to ensure the simulation remains responsive even at larger population sizes.

Requirements & Compatibility

• Python: Python 3.8+
• Libraries: numpy, matplotlib, customtkinter
• Operating Systems:
  • Windows 11: Tested
  • Linux: Tested, with some UI issues but works fine
  • macOS: Untested but should work fine as the script uses standard cross-platform libraries

Core Features

• Real-time Population Grid: A visual representation of the population where each colored square represents an individual of a specific allele.
• Dynamic Frequency Graphing: Line graph showing the population count of each allele over generations, updated in real-time.
• Interactive Control Suite: Start, pause, step, or run a specific number of generations to observe drift at your own pace.
• Stochastic Mutation Engine: Toggleable mutation rates to observe how new genetic variation interacts with random drift.
• Automated Fixation Detection: Option to automatically pause the simulation once a single allele has achieved fixation.

Architecture

The directory structure is organized to separate the mathematical model from the graphical user interface:

GeneticDriftSim/
├── gui.py              # CustomTkinter-based UI and Matplotlib rendering
├── main.py             # Main entry point and system configuration
└── simulator.py        # Wright-Fisher model logic and NumPy backend

Usage

git clone https://github.com/Scrimas/GeneticDriftSim
cd GeneticDriftSim
pip install -r requirements.txt
python main.py

License

This project is licensed under the MIT License.