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Matthew Stephens Lab Department of Human Genetics Department of Statistics University of Chicago Software program Multi-SNP evaluation for Genetic Association Reports, via Bayesian Variable Assortment Regression The software system piMASS (Posterior inference utilising Model Averaging and Subset Selection), created and taken care of by Yongtao Guan, implements MCMC-based inference strategies for Bayesian variable-selection regression described in Guan and Stephens (2011) This software was created to perform multi-SNP association analysis for enormous (genome-wide) datasets, even though it can also be applied to scaled-down association analysis information (e.g. candidate genes or areas), and in this case it types an different towards the multi-SNP association evaluation capabilities of BIMBAM (below). It might also be beneficial for Bayesian variable selection regression in large-scale issues a great deal more typically. Sparse Component Analysis (SFA) This software system makes use of ECME to compute a sparse, low-rank matrix factorization for any provided matrix,Office 2010 Professional Key, as described in:Engelhardt BE, Stephens M (2010) "Analysis of population structure: a unifying framework and novel practices based on sparse aspect analysis." PLoS Genetics 6(9):e1001117.Download C++ code and instructions for SFA 1.0 and further documentation for the SFA model.BIMBAM: software package for Bayesian IMputation-Based Association Mapping. The program BIMBAM implements solutions for assocation mapping, based mostly on those described in Servin, B and Stephens, M (2007). Imputation-based analysis of association scientific tests: candidate genes and quantitative traits. PLoS Genetics, 2007. BIMBAM can handle both sizeable association scientific tests (e.g., genome scans) and smaller sized research of candidate genes/regions. The computer software is distributed under the GNU Public License (GPL). To register and download, click here. Instructions are available here fastPHASE: software program for haplotype reconstruction, and estimating missing genotypes from population data The program fastPHASE implements systems described in Scheet, P and Stephens, M (2006). A fast and flexible statistical model for large-scale population genotype information: applications to inferring missing genotypes and haplotypic phase. Am J Hum Genet fastPHASE can handle larger data-sets than PHASE (e.g., hundreds of thousands of markers in thousands of individuals), but does not provide estimates of recombination rates. Our experiments suggest that haplotype estimates are slightly less accurate than from PHASE, but missing genotype estimates appear to be similar or even slightly better than PHASE. The software system is free for non-commercial use, and may be licensed for commercial use. To view the terms and conditions, and then proceed to download, click here. PHASE: program for haplotype reconstruction, and recombination rate estimation from population information The program PHASE implements techniques for estimating haplotypes from population genotype information described in Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian practices for haplotype reconstruction from population genotype information. American Journal of Human Genetics, 73:1162-1169. Stephens, M.,Microsoft Office Professional Plus 2007, Smith,Office 2007 Professional Plus Key, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population information. American Journal of Human Genetics, 68, 978--989. Stephens, M., and Scheet, P. (2005). Accounting for Decay of Linkage Disequilibrium in Haplotype Inference and Missing-Data Imputation. American Journal of Human Genetics, 76:449-462. The program also incorporates approaches for estimating recombination rates,Office Professional Plus, and identifying recombination hotspots: Crawford et al (2004). Evidence for substantial fine-scale variation in recombination rates across the human genome. Nature Genetics,. The software package is free for non-commercial use, and might be licensed for commercial use. To view the terms and conditions, and then proceed to download, click here. Instructions for PHASE are included on the download site, or are also available here. SCAT: Smoothed and Continuous AssignmenTs The program SCAT (Smoothed and Continuous AssignmenTs) implements a Bayesian statistical method for estimating allele frequencies and assigning samples of unknown (or known) origin across a continuous range of locations, based on genotypes collected at distinct sampling locations. In brief, the idea is to assume that allele frequencies vary smoothly in the study region, so allele frequencies are estimated at any offered location using observed genotypes at near-by sampling locations, with information at the nearest sampling locations being offered greatest weight. Details are offered in S K Wasser, A M Shedlock, K Comstock, E A Ostrander, B Mutayoba, and M Stephens. Assigning African elephant DNA to geographic region of origin: applications to the ivory trade. Proc Natl Acad Sci U S A, 41:14844-14852, 2004. SCAT is available here. HOTSPOTTER: computer software for identifying recombination hotspots from population SNP information This software package by Na Li implements practices from:
N Li and M Stephens. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism information. Genetics,Windows 7 Home Premium Key, 165(4)2213-2233, 2003. It is available free from here. Please direct comments and questions regarding HOTSPOTTER to Na Li, at wuolong SPAMBLOCKER AT gmail.com