Difference between revisions of "The Linear Mixed Models Toolbox"

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<strong>MediaWiki has been installed.</strong>
== Introduction ==


Consult the [https://www.mediawiki.org/wiki/Special:MyLanguage/Help:Contents User's Guide] for information on using the wiki software.
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 ==
{{lmt}} supports all models commonly used in genetic evaluation and has various options to handle genomic markers.


* [http://localhost/mediawiki/index.php/Intro Intro]
{{lmt}} has been used successfully for genetic evaluation data sets with >>200k genotyped animals, >>15m animals, >>500m equations.
* [http://localhost/mediawiki/index.php/Run_It Run It]


{{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,
thus easing to follow the structure of the parameter file even if it spans several tens of lines of code.


== Getting started ==
== Conditions of use ==
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Configuration_settings Configuration settings list]
{{lmt}} can be used by the scientific community free of charge, but users must credit {{lmt}}
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:FAQ MediaWiki FAQ]
in any publications.
* [https://lists.wikimedia.org/mailman/listinfo/mediawiki-announce MediaWiki release mailing list]
Commercial users must obtain the explicit approval of the author before using {{lmt}} and must credit {{lmt}} in any publication in scientific journals.
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Localisation#Translation_resources Localise MediaWiki for your language]
If {{lmt}} cannot be credited via citation the author must become a co-author.
* [https://www.mediawiki.org/wiki/Special:MyLanguage/Manual:Combating_spam Learn how to combat spam on your wiki]
 
== How to get it ==
 
{{lmt}} can be obtained '''on request''' from the [mailto:vinzent.boerner@qgg.au.dk 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 [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).
 
== [[supported features| Supported features]] ==
== [[Algorithms|Algorithms]] ==
== [[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).

Supported features

Algorithms

Parameter file terminology

Linear mixed models in lmt

Genomic data lmt

File formats

Input files

Output files

How to run it

Examples

Parameter file elements