README.md
- Author: Vito Dichio
- email: dichio.vito@gmail.com
- Last Modified: 24 March 2023
Source code for Dichio, V., Zeng, H. L., & Aurell, E. Statistical genetics in and out of quasi-linkage equilibrium. Reports on Progress in Physics (2023).
Based on FFPopSim (Python 2.7 & C++): Zanini, F., & Neher, R. A. (2012). FFPopSim: an efficient forward simulation package for the evolution of large populations. Bioinformatics, 28(24), 3332-3333. Installation required.
PLM-DCA (MATLAB & C++) for PLM inference as in in Gao, C. Y., Cecconi, F., Vulpiani, A., Zhou, H. J., & Aurell, E. (2019). DCA for genome-wide epistasis analysis: The statistical genetics perspective. Physical biology, 16(2), 026002. The source code is available at https://github.com/gaochenyi/CC-PLM.
myevolution.py simulates evolution by exploiting FFPopSim. Various instantaneous and/or all-time plots can be chosen.
crystalball.py old version of myevolution.py, contains (optionally) the inference step.
evol_plotter.py contains the source code for the plots that appear in the report.