The Linear Mixed Models Toolbox

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The Linear mixed Models Toolbox (lmt) is a stand-alone single executable software for for large scale linear mixed model analysis.

lmt supports all models commonly used in genetic evaluation and has various options to handle genomic markers.

lmt has been used successfully for genetic evaluation data sets with >>200k genotyped animals, >>15m animals, >>500m equations.

lmt is only available for 64 bit Linux operation systems, is run from the Linux command line, and uses an xml style parameter file which is supposed to allow for an easy understanding by the user. Further using xml comes with support for automated commenting, uncommenting, 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.

Conditions of use

lmt can be used by the scientific community free of charge, but users must credit lmt in any publications. Commercial users must obtain the explicit approval of the author before using lmt and must credit lmt in any publication in scientific journals. If lmt cannot be credited via citation the author must become a co-author.

How to get it

lmt can be obtained on request from the author.

Feedback and support

lmt comes without any guaranteed support and the user is strongly advised to study the manual thoroughly. However, the author appreciates feedback about the program functionality, possible aborts (segmentation faults), usability of output and comprehensiveness of the manual.

For feedback, wish list, questions and support contact checked) or checked).

Supported features


Parameter file terminology

Linear mixed models in lmt

Genomic data lmt

File formats

Input files

Output files

How to run it


Parameter file elements