Difference between revisions of "The Linear Mixed Models Toolbox"
| (One intermediate revision by one other user not shown) | |||
| Line 2: | Line 2: | ||
The <b>L</b>inear mixed <b>M</b>odels <b>T</b>oolbox ({{lmt}}) is a stand-alone single executable software for for large scale linear mixed model analysis. | The <b>L</b>inear mixed <b>M</b>odels <b>T</b>oolbox ({{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 [https://www.w3schools.com/xml/ xml] style parameter file which is supposed to allow for an easy understanding by the user. Further using [https://www.w3schools.com/xml/ xml] comes with support for automated commenting, uncommenting, indentation, code-folding and syntax highlighting by almost every editor, | |||
an [https://www.w3schools.com/xml/ xml] style parameter file which is supposed to allow for | thus easing to follow the structure of the parameter file even if it spans several tens of lines of code. | ||
by the user. Further using [https://www.w3schools.com/xml/ xml] comes with support for automated commenting, | |||
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 [mailto:vinzent.boerner@qgg.au.dk author]. | |||
{{lmt}} can be | |||
== Feedback and support == | == Feedback and support == | ||
| Line 40: | Line 25: | ||
However, the author appreciates feedback about the program functionality, possible aborts (segmentation faults), usability of output and comprehensiveness of the manual. | However, the author appreciates feedback about the program functionality, possible aborts (segmentation faults), usability of output and comprehensiveness of the manual. | ||
==[[supported features| Supported features]] == | For feedback, wish list, questions and support contact [mailto:vinzent.boerner@qgg.au.dk vinzent.boerner@qgg.au.dk](infrequently checked) or [mailto:vinzent.boerner@gmx.de vinzent.boerner@gmx.de](frequently checked). | ||
== [[Parameterfile1| Parameter file terminology | |||
== [[linear mixed | == [[supported features| Supported features]] == | ||
== [[Input | == [[Algorithms|Algorithms]] == | ||
== [[Run_It| | == [[Parameterfile1| Parameter file terminology]] == | ||
== [[ | == [[linear mixed models in lmt| Linear mixed models in lmt]] == | ||
== [[Genomic data in lmt| Genomic data lmt]] == | |||
== [[File formats|File formats]] == | |||
== [[Input files|Input files]] == | |||
== [[Output files|Output files]] == | |||
== [[Run_It|How to run it]] == | |||
== [[Examples|Examples]] == | |||
== [[Parameter file elements| Parameter file elements]] == | |||
Latest revision as of 00:58, 12 May 2022
Introduction
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 vinzent.boerner@qgg.au.dk(infrequently checked) or vinzent.boerner@gmx.de(frequently checked).