mateRNAl is an RNA evolutionary simulation tool implemented in Python. Simulations can be based on two fitness measurements: base pair distance to a target, or energy of MFE structure on sequence. Simulations can also be constrained to only allow sequences with a specified GC content.
- python 2.7+
- begins 0.9
- Vienna RNA package 2.0+
Print the help menu and options:
python mateRNAl.py -h
Default run:
python mateRNAl.py
Energy based selection on sequences of length 100 with GC content of 0.3, mutation rate of 0.1, and 2000 generations.
python mateRNAl.py -l 100 -g 0.3 -m 0.1 -t 2000
When a simulation is to be repeated with the same parameters, the -r flag tells mateRNAl how many replicates to run. Replicate runs can be run in parallel using -p to specify number of processes to use.
python mateRNAl.py -l 100 -g 0.3 -m 0.1 -t 2000 -n 5 -p 5
Each run produces a .csv file that can be easily parsed with tools such as pandas. Each column of the csv is labeled as follows:
generation, sequence, structure, energy, probability, gc, mutations,
@article{oliver2019emergence,
title={On the emergence of structural complexity in RNA replicators},
author={Oliver, Carlos G and Reinharz, Vladimir and Waldisp{\"u}hl, J{\'e}r{\^o}me},
journal={RNA},
volume={25},
number={12},
pages={1579--1591},
year={2019},
publisher={Cold Spring Harbor Lab}
}