Wrestling with a WOMBAT: Selected new features for linear mixed model analyses in the genomic age

Abstract

The software package WOMBAT has undergone considerable changes since its release in 2006. We describe its adaptation to multi-threaded processing and outline selected capabilities that have been added recently. Firstly, expanded features for multivariate analyses considering more than a few traits are available. These offer the facility for restricted maximum likelihood estimation subject to a penalty on the likelihood to reduce sampling errors. Furthermore options for analyses of overlapping subsets of traits and subsequent 'pooling' of estimates based on likelihood principles are provided. Secondly, special modules have been added for the iterative solution of larger sets of mixed model equations, incorporating genomic information in a single-step analysis. These include options for analyses fitting the standard breeding value model or the so-called hybrid model. In addition, auxiliary calculations to obtain the genomic or joint relationship matrix (or inverse thereof) for animals with and without genotypes are available.