Tag: Haplotype

HapMiner 1.1 – Haplotype-based Linkage Disequilibrium mapping via direct Data Mining

HapMiner 1.1

:: DESCRIPTION

HapMiner is a computer program for association mapping based on directly mining the haplotypes from case-control data via a density-based clustering algorithm. HapMiner can be applied to whole-genome screens, as well as candidate-gene studies in small genomic regions.

::DEVELOPER

Jing Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux

:: DOWNLOAD

 HapMiner

:: MORE INFORMATION

Citation

Li and Jiang (2005),
“Haplotype-based linkage disequilibrium mapping via direct data mining”
Bioinformatics, 21(24):4384-4393.

HapTagger – Tag SNP Selection Using Haplotype

HapTagger

:: DESCRIPTION

HapTagger is a software for finding tag SNPs. HapTagger is compared with existing methods as well as the official tagging tool (called Haploview) of the International HapMap project using a variety of real data sets.

::DEVELOPER

Kun-Mao Chao

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java 

:: DOWNLOAD

 HapTagger

:: MORE INFORMATION

Citation

Huang, Y.-T. and Chao, K.-M., 2008,
“A New Framework for the Selection of Tag SNPs by Multimarker Haplotypes”
Journal of Biomedical Informatics, 6: 953-961.

 

HMC 0.9.1 – Haplotype Inference tool based on Markov Chain model

HMC 0.9.1

:: DESCRIPTION

HMC (Haplotype Inference Based on Markov Chain)is a new haplotype inference methods based on Markov chain model which do not assume haplotype blocks in the population and allows each individual haplotype to have its own structure, thus are able to accommodate recombination and obtain higher adaptivity to the genotype data, specifically in the case of long marker maps. The proposed method presents a general Markov chain model for haplotype inference problem. A dynamic programming algorithm is developed for the model. The algorithm is theoretically guaranteed to find exact global optimal solutions within polynomial running time. Through extensive computational experiments on simulated and real genotype data, the designed algorithm is shown to be efficient, and outperforms previous methods.

::DEVELOPER

APORC

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

  HMC

:: MORE INFORMATION

Citation

Ling-Yun Wu, Ji-Hong Zhang, and Raymond Chan.
Improved approach for haplotype inference based on Markov chain.
In Proceedings of 2nd International Symposium on Optimization and Systems Biology, Lecture Notes in Operations Research, Vol. 9, pp. 204–215, World Publishing Corporation, Beijing, 2008.

 

HAPPY 1.2 – Reconstruct HAPlotYpes

HAPPY  1.2

:: DESCRIPTION

HAPPY is a software package for Multipoint QTL Mapping in Genetically Heterogeneous Animals

::DEVELOPER

Richard Mott

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 HAPPY

:: MORE INFORMATION

Citation

Mott et al (2000)
“A new method for fine-mapping quantitative trait loci in outbred animal stocks”
Proc. Natl. Acad. Sci. USA, Proc Natl Acad Sci USA, 97(23):12649-12654.

HapForest – Forest for Detecting Haplotypes and Interactions

HapForest

:: DESCRIPTION

HapForest implements a forest-based approach to accommodate the haplotype uncertainties and variable importance to sort out significant haplotypes and their interactions in genomewide case-control association studies.

::DEVELOPER

The Collaborative Center for Statistics in Science(C2S2)

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Java

:: DOWNLOAD

 HapForest

:: MORE INFORMATION

Citation:

X. Chen, C.-T. Liu, M. Zhang and H.P. Zhang.
A forest-based approach to identifying gene and gene-gene interactions,
PNAS, 104: 19199–19203, 2007.

FAMHAP 19 beta – Haplotype Association Analysis Software

FAMHAP 19 beta

:: DESCRIPTION

FAMHAP is a software for single-marker analysis and, in particular, joint analysis of unphased genotype data from tightly linked markers (haplotype analysis).

::DEVELOPER

Tim Becker , Institute for Medical Biometry, Informatics and Epidemiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 FAMHAP

:: MORE INFORMATION

Citation

Herold C, Becker T (2009)
Genetic association analysis with FAMHAP: a major program update.
Bioinformatics 1;25(1):134-6

HTR – Haplotype Trend Regression

HTR

:: DESCRIPTION

HTR is an Haplotype/Trait Association Software.

::DEVELOPER

Dmitri Zaykin

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux

:: DOWNLOAD

 HTR

:: MORE INFORMATION

Citation:

Zaykin DV, Westfall PH, Young SS, Karnoub MC, Wagner MJ, Ehm MG (2002),
“Testing association of statistically inferred haplotypes with discrete and continuous traits in samples of unrelated individuals“,
Human Heredity, 53:79-91.

HAPLOT 3.2 – Graphical Presentation of Haplotype Block Structures

HAPLOT 3.2

:: DESCRIPTION

HAPLOT is a simple program for graphical presentation of haplotype block structures, tagSNP selection and SNP variation.

::DEVELOPER

Kidd Lab

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Java

:: DOWNLOAD

 HAPLOT

:: MORE INFORMATION

Citation

Sheng Gu, Andrew J. Pakstis and Kenneth K. Kidd
HAPLOT: a graphical comparison of haplotype blocks, tagSNP sets and SNP variation for multiple populations
Bioinformatics. 2005 Oct 15;21(20):3938-9.

HaploRec 2.3 – Haplotype Population-based Genotype data

HaploRec 2.3

:: DESCRIPTION

HaploRec is a statistical haplotype reconstruction algorithm targeted for large-scale disease association studies. It is especially suitable for data sets with a large number of subjects and a large number of possibly sparsely located markers.

::DEVELOPER

Group of Data mining in genetics 

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux /MacOsX
  • Java

:: DOWNLOAD

 HaploRec

:: MORE INFORMATION

Citation

Lauri Eronen, Floris Geerts, Hannu Toivonen.
HaploRec: Efficient and accurate large-scale reconstruction of haplotypes.
BMC Bioinformatics 7:542, 2006.

DASH 1.1.0 – DASH Associates Shared Haplotypes

DASH 1.1.0

:: DESCRIPTION

DASH (DASH Associates Shared Haplotypes) builds upon pairwise IBD shared segments to infer clusters of IBD individuals. Briefly, for each locus, DASH constructs a graph with links based on IBD at that locus, and uses an iterative min-cut approach to identify clusters. These are densely connected components, each sharing a haplotype. As DASH slides the local window along the genome, links representing new shared segments are added and old ones expire; these changes cause the resultant connected components to grow and shrink.

::DEVELOPER

Sasha Gusev 

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 DASH

:: MORE INFORMATION

Citation

Alexander Gusev, Eimear E. Kenny, Jennifer K. Lowe, Jaqueline Salit, Richa Saxena, Sekar Kathiresan, David M. Altshuler, Jeffrey M. Friedman, Jan L. Breslow, Itsik Pe’er.
DASH: A Method for Identical-by-Descent Haplotype Mapping Uncovers Association with Recent Variation,
The American Journal of Human Genetics 2011 Volume 88, Issue 6, 706-717

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