HaploPool – Estimate Haplotype Frequencies from Genotypes / DNA Pools

HaploPool

:: DESCRIPTION

HaploPool is a program for estimating haplotype frequencies either from genotypes of individuals or from genotypes of pooled individuals. The genotypes must be for a block of bi-allelic SNPs (meaning that the SNPs should be in linkage disequilibrium with each other). The program assumes that it is given many genotypes of unrelated diploid individuals in Hardy-Weinberg equilibrium. If the genotypes are from pooled DNA, the program assumes that every pool contains the same number of individuals and the individuals were chosen at random when placed into the pools. For a reasonable running-time, the number of individuals in a pool needs to be between 2 and 4.

::DEVELOPER

Computational Genetics Group

:: REQUIREMENTS

:: DOWNLOAD

HaploPool

:: MORE INFORMATION

Citation:

Kirkpatrick, B, Santos-Armendariz, C., Karp, R.M., and Halperin, E.
HaploPool: Improving Haplotype Frequency Estimation through DNA Pools and Phylogenetic Modeling.
Bioinformatics. 23: 3048-3055. 2007.

PoooL 1.1 – Estimate Haplotype Frequencies from large DNA Pools

PoooL 1.1

:: DESCRIPTION

PoooL is a novel constrained EM algorithm to estimate frequencies of single-nucleotide polymorphism (SNP) haplotypes from DNA pools. A quantity called importance factor is introduced to measure the contribution of a haplotype to the likelihood. Under the assumption of asymptotic normality of the estimated allele frequencies and a system of linear constraints on haplotype frequencies the importance factor remains a constant in the iterative maximization process.

::DEVELOPER

Han Zhang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

 PoooL

:: MORE INFORMATION

Citation

Han Zhang, Hsin-Chou Yang and Yaning Yang
PoooL: An efficient algorithm for estimating haplotype frequencies from large DNA pools
Bioinformatics 2008 24(17):1942-1948