Generalized gametic relationships - a guide to practical implementation

Method: The guide to practical application of generalized gametic relationships has three main parts. The first is the source code (Fortran2015) of a program for setting up the inverse of a generalized gametic relationship matrix from pedigree data, a detailed program description and example input and output files. In the second part six worked examples are presented, demonstrating in very detail how various mixed models with generalized gametic relationship matrices can be implemented using the ASReml package. Each example is accompanied by R-code to check model details and the correctness of the ASReml implementation. Finally a large mouse data set (about 13,000 observations on body weight, 153 generations) is provided together with details on how it can be analyzed with different gametic models using ASReml.