MuGen is a C++ library that implements a comprehensive approach to Bayesian inference of multi-trait models for quantitative genetics. It enables genome-wide association studies and genome-enabled prediction, allows for complicated and unbalanced experimental designs, outlier observations, and missing data. However, while motivation for the construction of this library was to model genetic data, other types of data that could benefit from hierarchical treatment can also be analyzed. This library depends on the GNU Scientific Library and therefore is under the GNU General Public License, unlike most of our software that we release under the more permissive BSD 3-clause license. A major revision of this library is in the works, with planned elimination of the GSL dependency and the GPL.