polyDFE provides a flexible statistical framework to estimate the DFE and alpha from SFS data, by fitting several types of probability distributions.
The files provided here can be used to run the analysis presented in the polyDFE chapter:
- central chimpanzee data:
- central_chimp_sfs
- files used for running polyDFE:
- init_A.txt
- init_C.txt
- params_basinhop.txt
- overview of runs of polyDFE for a full analysis:
- run_polyDFE.txt
- polyDFE output files:
- central_chimp_A
- central_chimp_A.txt
- central_chimp_A_no_div.txt
- central_chimp_C.txt
- central_chimp_C_no_div.txt
- central_chimp_Del.txt
- central_chimp_Del_no_div.txt
- bootstrap datasets:
- boostrap_central_1
- central_chimp_sfs_1
- R script containing the full analysis of the polyDFE output:
- analysis.R
polyDFE can be downloaded from GitHub