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The snphap application is available to registered users only. If you aren't registered but would like to run this program using our facilities, Register Now!
This program implements a fairly standard method for estimating haplotype frequencies using data from unrelated individuals. It uses an EM algorithm to calculate ML estimates of haplotype frequencies given genotype measurements which do not specify phase. The algorithm also allows for some genotype measurements to be missing (due, for example, to PCR failure). It also allows multiple imputation of individual haplotypes.
For a large number of loci, the number of possible haplotype instances rapidly becomes impossibly large. This program avoids this difficulty by starting by fitting 2-locus haplotypes and extending the solution by one locus at a time.
Detailed description of snphap
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