:: DESCRIPTION
HAP is an extension of SNPHAP. It is a software for haplotype analysis of polymorphic markers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhao, J. H. (2004)
“2LD, GENECOUNTING and HAP: Computer programs for linkage disequilibrium analysis“.
Bioinformatics, 20, 1325-1326
:: DESCRIPTION
GENECOUNTING is a software of gene-counting for haplotype analysis with permutation tests for global association and specific haplotypes, accounting for missing data
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhao, J. H, .Lissarrague, S., Essioux, L., Sham, P. C. (2002)
“GENECOUNTING: haplotype analysis with missing genotypes”
Bioinformatics, 18(12), 1694-1695.
:: DESCRIPTION
HPlus is a user-friendly software application for estimating haplotype frequencies, inferring individual haplotypes, and most significantly assessing haplotypic associations with various types of phenotypes. HPlus handles bi-allelic genetic markers such as SNPs, and multi-allelic genetic markers such as microsatellites.
::DEVELOPER
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Zhao, Li, Khalid (2003),
“A method for assessing disease associations with SNP haplotypes and environmental variables in case-control“,
American Journal of Human Genetics, 72(5):1231-1250.
:: DESCRIPTION
The disentangler is a visualization technique for linkage disequilibrium mapping and haplotype analysis of multiple multi-allelic genetic markers.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
N. Kumasaka, Y. Okada, A. Takahashi, M. Kubo, Y. Nakamura and N. Kamatani.
Disentangler: a visualization technique for linkage disequilibrium mapping using multi-allelic loci ;
(Abstract / Program #708F). Presented at the 12th International Congress of Human Genetics/61st Annual Meeting of The American Society of Human Genetics, October 14, 2011, Montreal, Canada.
:: DESCRIPTION
IQLS (Incomplete-Data Quasi-likelihood Score Test) is a C++ program that performs haplotype frequency estimation and case-control association testing between a binary trait and haplotypes of multiple tightly-linked SNPs. A special feature of IQLS is that both related and unrelated individuals can be included in the case-control sample. The user specifies the number of SNPs in the sliding haplotype window, and for each set of SNPs, the IQLS program computes haplotype frequency estimates and both 1-df and full-df tests for haplotype association with a case-control phenotype. The IQLS software is suitable for case-control haplotype analysis in outbred samples with arbitrary combinations of related and unrelated individuals, including large pedigrees, provided that the relationships are known.
::DEVELOPER
Zuoheng Wang and Mary Sara McPeek
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Wang, Z., and McPeek,M.S. (2009).
An incomplete-data quasi-likelihood approach to haplotype-based genetic association studies on related individuals.
J. Am. Stat. Assoc. 104, 1251-1260.
Wang, Z., and McPeek, M.S. (2009).
ATRIUM: Testing untyped SNPs in case-control association studies with related individuals.
Am. J.Hum. Genet. 85, 667-678.
