The program PHASE implements methods for estimating haplotypes from population genotype data described in Stephens, M., and Donnelly, P. (2003). A comparison of Bayesian methods for haplotype reconstruction from population genotype data. 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., 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 also incorporates methods 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 is free for non-commercial use, and may be licensed for commercial use

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