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Matthew Stephens Lab Department of Human Genetics Division of Statistics University of Chicago Program Multi-SNP analysis for Genetic Association Research, via Bayesian Variable Collection Regression The software piMASS (Posterior inference by using Product Averaging and Subset Selection), written and taken care of by Yongtao Guan, implements MCMC-based inference systems for Bayesian variable-selection regression described in Guan and Stephens (2011) This application was developed to accomplish multi-SNP association evaluation for massive (genome-wide) datasets, even though it can also be applied to smaller association analysis information (e.g. candidate genes or regions), and with this case it kinds an solution on the multi-SNP association analysis capabilities of BIMBAM (beneath). It might also be handy for Bayesian variable variety regression in large-scale complications alot more normally. Sparse Aspect Analysis (SFA) This software makes use of ECME to compute a sparse, low-rank matrix factorization for the presented matrix, as described in:Engelhardt BE, Stephens M (2010) "Analysis of population structure: a unifying framework and novel options based on sparse factor analysis." PLoS Genetics 6(9):e1001117.Download C++ code and instructions for SFA 1.0 and further documentation for the SFA model.BIMBAM: computer software for Bayesian IMputation-Based Association Mapping. The program BIMBAM implements procedures for assocation mapping, based mostly on those described in Servin, B and Stephens, M (2007). Imputation-based analysis of association reports: candidate genes and quantitative traits. PLoS Genetics, 2007. BIMBAM can handle both considerable association reports (e.g., genome scans) and smaller studies 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: computer software for haplotype reconstruction, and estimating missing genotypes from population info The program fastPHASE implements approaches described in Scheet, P and Stephens,Office 2007 Pro Plus Activation, M (2006). A fast and flexible statistical product 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 package is free for non-commercial use, and can 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 info The program PHASE implements systems for estimating haplotypes from population genotype data described in Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian strategies for haplotype reconstruction from population genotype information. American Journal of Human Genetics, 73:1162-1169. Stephens, M., Smith, N., and Donnelly, P. (2001). A new statistical method for haplotype reconstruction from population data. American Journal of Human Genetics, 68, 978--989. Stephens, M.,Office Professional Plus 2007, 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 software system also incorporates options for estimating recombination rates, 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 system is free for non-commercial use,Microsoft Office Professional Plus 2007 Product Key, and can be licensed for commercial use. To view the terms and conditions, and then proceed to download,Windows 7 Home Premium Product Key, 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 mostly 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 making use of observed genotypes at near-by sampling locations, with information at the nearest sampling locations being provided greatest weight. Details are presented 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 for the ivory trade. Proc Natl Acad Sci U S A, 41:14844-14852,Office Ultimate 2007 Product Key, 2004. SCAT is available here. HOTSPOTTER: software system for identifying recombination hotspots from population SNP data This computer software by Na Li implements practices from:
N Li and M Stephens. Modeling linkage disequilibrium and identifying recombination hotspots using single-nucleotide polymorphism information. Genetics, 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