Software

BOLT-LMM 1.0 [Download page]

BOLT-LMM (Loh et al. submitted bioRxiv) is a software package that computes statistics for testing association between phenotype and genotypes using a linear mixed model (LMM). By default, BOLT-LMM 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 methods, providing an opportunity for increased power to detect associations while controlling false positives. Additionally, BOLT-LMM applies algorithmic advances to compute association statistics much faster than existing methods.

ALDER 1.03 [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 1.01 [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.

CaBLAST / CaBLAT 0.9 [Download page]

Compression-accelerated BLAST (CaBLAST) and Compression-accelerated BLAT (CaBLAT) are two prototype implementations of alignment and sequence search algorithms that apply “compressive genomics” (Loh, Baym, and Berger 2012 Nat Biotech): i.e., they exploit redundancy in genomic data sets by compressing data in a way that allows direct computation on the compressed data.