GRain (version 2.2) is software intended to enable and promote testing of various hypotheses with respect to purging and heterogeneity of inbreeding depression. The program is based on a stochastic approach, the gene dropping method, and calculates various individual coefficients from large and complex pedigrees. To test the purging of inbreeding depression, GRain calculates, together with the “classical” inbreeding coefficient, ancestral inbreeding coefficients proposed by Ballou (1997) and Kalinowski et al. (2000) as well as an ancestral history coefficient, defined here for the first time. Ancestral history coefficient quantifies the frequency that an allele has undergone Identical by Descent (IBD) status in the past. Furthermore, GRain enables testing of heterogeneity and/or purging of inbreeding depression with respect to different founders/ancestors as it calculates partial coefficients for all previously obtained coefficients.
The contents of this directory provide the GRain source code, compiled GRain program for Windows, source code for the R interface and exampe data files.In addition a short manual is provided at the beginning of the GRain.f90 source code file.
Detailed descriptions of the program methods, input and output files for the GRain v2.1 are provided in the paper:
Roswitha Baumung , János Farkas, Didier Boichard, Gábor Mészáros, Johann Sölkner, Ino Curik (2015) GRain: A Computer Program to Calculate Ancestral and Partial Inbreeding Coefficients using a Gene Dropping Approach, Journal of Animal Breeding and Genetics, 132, 100-108. doi:10.1111/jbg.12145
Unfortunately, the GRain v2.1 had a small bug in the calculation of the Kalinowski ancestral and new inbreeding coefficients which has been corrected in the GRain v2.2.
Detailed descriptions of the required corrections made in the GRain v2.2 are provided in the paper:
Doekes HP, Curik I, Nagy I, Farkas J, Kövér Gy, Windig JJ. Revised calculation of Kalinowski’s ancestral and new inbreeding coefficients. Diversity. 2020;(accepted).
The full text is available from the authors on demand.