Quantifying the impact of changes in effective population size and expression level on the rate of coding sequence evolution
Thibault Latrille, Nicolas Lartillot,
Theoretical population biology, Volume 142, pages 57-66
https://doi.org/10.1016/j.tpb.2021.09.005
LaTeX for the manuscript and figures are available at https://github.com/ThibaultLatrille/PhD/tree/master/GenotypePhenotypeFitness
This repository is meant to provide the necessary scripts and data to reproduce the figures shown in the manuscript. The experiments can either run on a local computer or in a cluster configuration (slurm).
The experiments are meant to run on Linux/Unix/MacOS operating systems.
If problems and/or questions are encountered, feel free to open issues.
Clone the repository and cd to the dir.
git clone https://github.com/ThibaultLatrille/GenotypePhenotypeFitness
cd GenotypePhenotypeFitness
Install the compiling toolchains:
sudo apt install -qq -y make cmake clang
Clone and compile the C++ code for SimuEvol
git clone https://github.com/ThibaultLatrille/SimuEvol && cd SimuEvol && git checkout v1.0 && make release && cd ..
Install python3 packages
sudo apt install -qq -y python3-dev python3-pip screen
pip3 install snakemake numpy matplotlib statsmodels pandas ete3 --user
To reproduce a figures of the manuscript, one can use the config files of the simulations (.yaml).
python3 ./scripts/simulated_experiment.py --folder Heatmap --config figure-3D.yaml --nbr_cpu 4
The script simulated_experiment.py also contains options to run the simulations on a cluster (slurm).
To reproduce all the figures of the manuscript, this loop run all of them.
for FOLDER in "Heatmap" "Scaling" "Relaxation"; do
for CONFIG in ${FOLDER}/*.yaml; do
python3 ./scripts/simulated_experiment.py --folder${FOLDER} --config $(basename "${CONFIG}") --nbr_cpu 4
done
done
Once the run are completed, the script copy_artworks_after_run_all.sh copies the necessary figures in the manuscript folder.
sh ./copy_artworks_after_run_all.sh
Then the .tex files (main and supp. mat.) in the manuscript folder can be compiled with all figures.
You made modifications to one of the python script, a notebook, this README.md, or you added new features. You wish this work benefits to all (futur) users of this repository? Please, feel free to open a pull-request
You made modifications to the C++ code of the simulation framework SimuEvol. You wish this changes benefit to all users of these software?
Please, feel free to open pull-requests in the respective GitHub repository:
The MIT License (MIT)
Copyright (c) 2019 Thibault Latrille
Permission is hereby granted, free of charge, to any person obtaining a copy of this software and associated documentation files (the "Software"), to deal in the Software without restriction, including without limitation the rights to use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of the Software, and to permit persons to whom the Software is furnished to do so, subject to the following conditions:
The above copyright notice and this permission notice shall be included in all copies or substantial portions of the Software.
THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.