This package aims at simulating evolution in absence of mutation in gene or promoter sequences. It is based on the work by El Houdaigui et al., NAR 2019.
Clone the repository and run ourCode.py
All parameter files are in TwisTranscripT folder.
When you run the code, the following parameters will be asked:
path and name of the output csv file :
Type in the output csv file (ex: out.csv) or press enter if you do not want to save the results
Unit of length in base pairs that is deleted or inserted :
Type in an integer number. Please use a multiple of the simulation discretization length (60) and do not exceed 300
Probability for an evolutive event to be an inversion :
Type in a float between 0 and 1
Probability for an indel event to be an insertion:
Type in a float between 0 and 1
Number of generations :
Type in an integer. 500 generations run about 45 minutes.
Value of q :
Type in a value for q. Under 1e-5 will refuse all negative mutations, and above 2e-3 will accept almost all of them.