fastPHASE v. 1.2
new version coming soon (1 August, 2008)
fastPHASE is software (written in C and compiled on various platforms), which estimates haplotypes and missing genotypes from unphased multilocus SNP
genotype data obtained from unrelated individuals. In addition, the software
includes a variety of other features, such as the following:
detection of genotype errors
from unusual patterns of linkage disequilibrium; sampling of haplotypes and genotypes from their conditional distribution, given the observed data; incorporating
"subpopulation information" (e.g. distinct sampling locations) into analyses; estimation of sample haplotype frequencies; and more.
Our results show it to be competitive with the program PHASE in terms of haplotype accuracy and slightly better for imputing missing genotypes; however, it is potentially much faster and able to handle data from thousands of individuals at hundreds of thousands of SNP markers.
The methods for fastPHASE are described in:
Scheet, P and Stephens, M (2006) A Fast and Flexible Statistical Model for Large-Scale Population Genotype Data: Applications to Inferring Missing Genotypes and Haplotypic Phase. American Journal of Human Genetics 78: 629-644
Download
fastPHASE is free for non-commercial use. To view the license and then proceed to download, click here.
Additional Links
For questions or comments, please email fphase [at] washington [dot] edu