@article {Stephens2001,
	title = {{A new statistical method for haplotype reconstruction from population data.}},
	journal = {American journal of human genetics},
	volume = {68},
	number = {4},
	year = {2001},
	pages = {978{\textendash}89},
	abstract = {Current routine genotyping methods typically do not provide haplotype information, which is essential for many analyses of fine-scale molecular-genetics data. Haplotypes can be obtained, at considerable cost, experimentally or (partially) through genotyping of additional family members. Alternatively, a statistical method can be used to infer phase and to reconstruct haplotypes. We present a new statistical method, applicable to genotype data at linked loci from a population sample, that improves substantially on current algorithms; often, error rates are reduced by > 50\%, relative to its nearest competitor. Furthermore, our algorithm performs well in absolute terms, suggesting that reconstructing haplotypes experimentally or by genotyping additional family members may be an inefficient use of resources.},
	keywords = {Algorithms, Calibration, Computer Simulation, Gene Frequency, Gene Frequency: genetics, Haplotypes, Haplotypes: genetics, Humans, Research Design, Sensitivity and Specificity, Statistics as Topic},
	issn = {0002-9297},
	doi = {10.1086/319501},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1275651\&tool=pmcentrez\&rendertype=abstract},
	author = {Stephens, M and Smith, N J and Donnelly, P}
}
@article {Stephens2005,
	title = {{Accounting for decay of linkage disequilibrium in haplotype inference and missing-data imputation.}},
	journal = {American journal of human genetics},
	volume = {76},
	number = {3},
	year = {2005},
	pages = {449{\textendash}62},
	abstract = {Although many algorithms exist for estimating haplotypes from genotype data, none of them take full account of both the decay of linkage disequilibrium (LD) with distance and the order and spacing of genotyped markers. Here, we describe an algorithm that does take these factors into account, using a flexible model for the decay of LD with distance that can handle both "blocklike" and "nonblocklike" patterns of LD. We compare the accuracy of this approach with a range of other available algorithms in three ways: for reconstruction of randomly paired, molecularly determined male X chromosome haplotypes; for reconstruction of haplotypes obtained from trios in an autosomal region; and for estimation of missing genotypes in 50 autosomal genes that have been completely resequenced in 24 African Americans and 23 individuals of European descent. For the autosomal data sets, our new approach clearly outperforms the best available methods, whereas its accuracy in inferring the X chromosome haplotypes is only slightly superior. For estimation of missing genotypes, our method performed slightly better when the two subsamples were combined than when they were analyzed separately, which illustrates its robustness to population stratification. Our method is implemented in the software package PHASE (v2.1.1), available from the Stephens Lab Web site.},
	keywords = {Algorithms, Alleles, Biometry, Chromosomes, Data Interpretation, Genetic, Genomics, Genomics: statistics \& numerical data, Genotype, Haplotypes, Haplotypes: genetics, Human, Humans, Linkage Disequilibrium, Male, Models, Software, Statistical, X, X: genetics},
	issn = {0002-9297},
	doi = {10.1086/428594},
	url = {http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1196397\&tool=pmcentrez\&rendertype=abstract},
	author = {Stephens, Matthew and Scheet, Paul}
}
