BOLT-LMM and BOLT-REML [Download page]
The BOLT-LMM algorithm (Loh et al. 2015) rapidly computes statistics for association between phenotype and genotypes using a linear mixed model (LMM). The BOLT-REML algorithm partitions SNP-heritability and estimates genetic correlations using a Monte Carlo algorithm for fast multi-component, multi-trait modeling (Loh et al. bioRxiv). By default, BOLT-LMM association analysis assumes a Bayesian mixture-of-normals prior for the random effect attributed to SNPs other than the one being tested. This model generalizes the standard “infinitesimal” mixed model used by existing mixed model association methods, providing an opportunity for increased power to detect associations while controlling false positives.
ALDER [Download page]
ALDER (Loh, Lipson et al. 2012 Genetics) is a software package that computes weighted linkage disequilibrium (LD) curves, which can be used to infer admixture parameters including dates, mixture proportions, and phylogeny. This package extends the methodology of the ROLLOFF software in ADMIXTOOLS (Patterson et al. 2012).
MixMapper [Download page]
MixMapper (Lipson, Loh et al. 2012 MBE) is a software package that analyzes allele frequency correlations among multiple populations simultaneously to build a tree (or .admixture graph.) of population relationships that incorporates the possibility of mixture. This package complements the qpgraph software in ADMIXTOOLS, with the key difference that it semi-automatically searches the space of possible admixture graph topologies to find the best fit for the data.