The Linear Mixed Models Toolbox

The Linear mixed Models Toolbox (lmt) is a stand-alone single executable software for for large scale linear mixed model analysis. It is the successor of DMU, the well-known and widely used software package for linear mixed model analysis developed and maintained by Per Madsen and Just Jensen.

Since the early days of software development in statistics and quantitative genetics time has moved on in terms of what programming languages are capable of and therefore DMU has been given a thorough overhaul.

One result of the overhaul is the new name, lmt, resulting from the difficulty to translate the acronym DMU into something which is generally meaningful throughout time. For those who prefer the acronym DMU, they may refer to lmt as DMU-next.

The second area of the overhaul is the parameter file interface. lmt now comes with an xml style parameter file which is supposed to allow for a much easier understanding by the user. Further using xml comes with support for automated commenting, un- commenting, indentation, code-folding and syntax highlighting by almost every editor, thus easing to follow the structure of the parameter file even if it spans several tens of lines of code.

The third area of the overhaul is the program structure. DMU was structured into several programs (DMU1, DMU4, DMU5, DMUAI, RJMC). In contrast, lmt is meant to provide the functionalities all those programs via a single parameter file and a single executable.

While lmt is finally meant to be a full scale successor of DMU, it does not yet provide all its functionalities in some areas, in others it already provides more. More specifi- cally, there no REML facilities available yet, but large scale linear mixed model solving provides Single-Step-T-BLUP facilities, uploading of genotypes and building of genomic relationship matrices on the fly etc etc.

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