Repository for code associated with the preprint:
Predicting Parallelism and Quantifying Divergence in Experimental Evolution
https://www.biorxiv.org/content/10.1101/2020.05.13.070953v2
This project uses a number of publicly available datasets. Processed data is included in the Zenodo repository. All raw data has been previously published and will have to be accessed as described below.
An environment.yml file is in this repository and can be used to make the conda environment used to perform all analyses. To summarize, the analyses are primarily performed in Python 3.6 and require the following packages: numpy, pandas, matplotlib, scipy, Scikit-learn, Biopython, and networkx.
This repository also requires asa159.f90 source file which can be obtained from the FisherExact repository. The file asa159.f90 is written on fortran, so make sure you have a fortran compiler (gfortran) installed. See here ==> https://gcc.gnu.org/wiki/GFortranBinaries.
Once asa159.f90 is in ~/GitHub/ParEvol/Python, run the command:
f2py -c -m asa159 asa159.f90All the processed data is available on zenodo https://doi.org/10.5281/zenodo.3779341.
Below are instructions for obtaining the original dataset, though it is not necessary to redo the analyses.
Data from Tenaillon et al. (2012) can be obtained from their publication URL. For the mutation data you will need to download Table S2 as an excel file (1212986tableS2.xls) and convert it to CSV format. Move the CSV to ~/GitHub/ParEvol/data/Tenaillon_et_al. Table S1 in Tenaillon et al. (2019) contains the fitness estimates. It is in the supplement.
Data from Turner et al. (2018) can be obtained from the publication's Dryad repository. Move the data in the repository to ~/GitHub/ParEvol/data/Turner_et_al
Run the following command:
python clean_data.pypython run_simulations.pypython make_figs.pyOlivier Tenaillon, Alejandra Rodraguez-Verdugo, Rebecca L. Gaut, Pamela McDonald, Albert F. Bennett, Anthony D. Long, and Brandon S. Gaut. The Molecular Diversity of Adaptive Convergence. Science, 416335(6067): 457–461, 2012.
Caroline B. Turner, Christopher W. Marshall, and Vaughn S. Cooper. Parallel genetic adaptation across environments differing in mode of growth or resource availability. Evolution Letters, 2(4):355–367, August 2018.