This document was created as a repository of the scripts used in the analyses of the article: Wade, Kyriazis, Cavassim, Lohmueller. 2023. "Quantifying the fraction of new mutations that are recessive lethal." Evolution. (doi: XXXXX).
Files used in the pipeline are described as follow
- sim.slim Forward in time simulations were conducted using the software SLiM 31.
- demographic_inference.py This python script contains the code used for the inference demographic parameters using the software dadi2.
- selection_inference.py This python script contains the code used for the inference of the distribution of fitness effects (DFE) using the software fitdadi3.
Script for Table 1's complex model analysis:
- parse_inference_results_Table1.R
Table 1 Output:
- inference_results.table.aug.2022.llike_cutoff_20.txt
- inference_results.table.aug.2022.llike_cutoff_5.txt
Scripts for each figure are available in figures/scripts
Data produced to generate figures are:
- figures/data/all_inferences.csv
- figures/data/all_log_20_inferences.csv
- figures/data/exp_v_inferred.csv
- figures/data/sim_avg_sfs10.csv
- figures/data/sim_avg_sfs100.csv
- figures/data/sim_avg_sfs1000.csv
- figures/data/computed_avg_sfs10.csv
- figures/data/computed_avg_sfs100.csv
- figures/data/computed_avg_sfs1000.csv
Scripts for mutation-selection-drift balance results are available at: https://github.com/ckyriazis/lethals_scripts
References
- 1 Haller, Benjamin C., and Philipp W. Messer. 2019. “SLiM 3: Forward Genetic Simulations Beyond the Wright–Fisher Model.” Molecular Biology and Evolution 36 (3): 632–37.
- 2 Gutenkunst, Ryan, Ryan Hernandez, Scott Williamson, and Carlos Bustamante. 2010. “Diffusion Approximations for Demographic Inference: DaDi.” Nature Precedings, June, 1–1.
- 3 Kim, Bernard Y., Christian D. Huber, and Kirk E. Lohmueller. 2017. “Inference of the Distribution of Selection Coefficients for New Nonsynonymous Mutations Using Large Samples.” Genetics 206 (1): 345–61.