Eagle [Download page]

The Eagle algorithm (Loh et al. bioRxiv) estimates haplotype phase given diploid genotype data from large population cohorts (tens to hundreds of thousands of samples) typed on genotyping arrays. In contrast to conventional HMM-based methods for statistical phasing, Eagle applies long-range phasing to rapidly phase segments of genome identical-by-descent (IBD) among closely or distantly related individuals within the sample; in very large samples, such IBD is pervasive. To phase segments lacking IBD, Eagle then runs two iterations of fast approximate Viterbi decoding using a simple diploid analog of the Li-Stephens HMM.

BOLT-LMM and BOLT-REML [Download page]

The BOLT-LMM algorithm (Loh et al. 2015 Nat Genet) 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. in press Nat Genet). 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. 2013 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. 2013 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.