Table 2.
Useful software for genome-wide eQTL analysis using mixed models.
| Program | Method and algorithm | Website (http) | MA1 | Source code | Reference |
|---|---|---|---|---|---|
| GCTA | Average information restricted maximum likelihood (AIREML) | cnsgenomics.com/software/gcta | Δ | C++ | Yang et al., 2011 |
| GEMMA | Newton–Raphson restricted maximum likelihood (NRREML) Bayesian using Metropolis and Hastings | www.xzlab.org/software.html | O | C++ | Zhou and Stephens, 2014 Zhou et al., 2013 |
| TASSEL | NRREML | www.maizegenetics.net/tassel | X | Java | Zhang et al., 2010 |
| MTG2 | AIREML | sites.google.com/site/honglee0707/mtg2 | O | FORTRAN | Lee and van der Werf, 2016 |
| GENSEL | Bayesian using Gibbs sampling | archive.is/bigs.ansci.iastate.edu | X | C++ | Kizilkaya et al., 2010 |
| MMAP | AIREML, NRREML, Expectation-maximization restricted maximum likelihood, Fisher information restricted maximum likelihood | mmap.github.io | X | Undisclosed | O’Connell, 2014 |
| FaST-LMM | Maximum likelihood2, Restricted maximum likelihood2 | www.microsoft.com/en-us/research/project/fastlmm | X | Python | Lippert et al., 2011 |
1Multivariate analysis; Δ indicates that bivariate analysis is available.
2Spectral decomposition-based algorithm is employed.