By: Luis Rodrigo Arce-Valdés (01-30-22)
SimuDrift.py is a simple genetic drift simulator python 3 script. This program creates plots of simulations of changes in allelic frequencies across generations as a function of initial effective population size and initial allelic frequencies. The program assumes a Fisher-Wright-like closed population of haploid organisms with non-overlapping generations, mutations or natural selection.
Before attempting to run this script you need to have installed on your computer Python3, and the numpy and matplotlib modules.
Follow this tutorial to learn how to install python modules. Personally, I prefer to use conda as environmental manager insted of installing using pip. If you wish to install using conda, here is the documentation of Miniconda: thre free minimal installer of conda. After installing it. You can use conda to install the required modules using:
conda install -c anaconda numpy
conda install -c conda-forge matplotlib
Simply download the SimuDrift.py script and run it via a Unix terminal using:
python SimuDrift.py
For Windows users I found this tutorial explaining how to use Python.
After running the script, the program will automatically ask the user for the input of the following parameters:
- Number of A1 alleles in the population. These are the alleles that the program track their relative frequency.
- Number of A2 alleles in the population. The frequency of this other alleles are easily estimated as: q = 1 - p.
- Number of generations. For how many generations will the program run?
- Number of simulations. How many simulations will the program do?
All of these parameters must be inputed as an integer higher than 0 for the program to run!
