Table 2.

Mixed model association software.

Software	Authors	Website
DOQTL	Aulchenko et al. 2007; Amin et al. 2007; Svishcheva et al. 2012; Belonogova et al. 2013	http://cgd.jax.org/apps/doqtl/DOQTL.shtml
GRAMMAR		http://www.genabel.org/packages/GenABEL
Qtlrel	Cheng et al. 2011	http://cran.r-project.org/web/packages/QTLRel/
dlmap	Huang et al. 2012	http://cran.r-project.org/web/packages/dlmap/index.html
MASTOR	Jakobsdottir and McPeek 2013	http://www.stat.uchicago.edu/~mcpeek/software/MASTOR/index.html
EMMA	Kang et al. 2008	http://genetics.cs.ucla.edu/emma/
EMMAX	Kang et al. 2010	http://genetics.cs.ucla.edu/emmax/
MTMM	Korte et al. 2012	https://cynin.gmi.oeaw.ac.at/home/resources/mtmm (ASREML)
Mendel	Lange et al. 2013	http://www.genetics.ucla.edu/software/mendel
FaST-LMM	Lippert et al. 2011; Listgarten et al. 2013	http://fastlmm.codeplex.com/
WOMBAT	Meyer 2007; Meyer and Tier 2011	http://didgeridoo.une.edu.au/km/wombat.php
Qxpak.5	Pérez-Enciso and Misztal 2011	http://www.icre.cat/Web/OtherSectionViewer.aspx?key=485&titol=Software:%20Qxpak&researcher=255
LMM-Lasso	Rakitsch et al. 2013	http://webdav.tuebingen.mpg.de/u/karsten/Forschung/research.html?page=research&topic=LMM-Lasso&html=text
MLMM	Segura et al. 2012	https://github.com/bvilhjal/mixmogam (Python), https://cynin.gmi.oeaw.ac.at (R)
wgaim	Taylor and Verbyla 2011	http://cran.r-project.org/web/packages/wgaim/index.html
ROADTRIPS	Thornton and McPeek 2010	http://www.stat.uchicago.edu/~mcpeek/software/ROADTRIPS/index.html
GCTA	Yang et al. 2011	http://www.complextraitgenomics.com/software/gcta/
TASSEL	Yu et al. 2005; Zhang et al. 2010	http://www.maizegenetics.net/index.php?option=com_content&task=view&id=89&Itemid=119
GEMMA	Zhou and Stephens 2012	http://home.uchicago.edu/xz7/software.html

Links to download currently available mixed model association software and corresponding references.