Ligate Haplotypes 0.04 – Ligate Haplotypes with Two Overlapping Regions

Ligate Haplotypes 0.04

:: DESCRIPTION

Ligate Haplotypes is a perl software to ligate haplotypes with two overlapping regions

::DEVELOPER

Yun Li

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Perl
:: DOWNLOAD

 Ligate Haplotypes

:: MORE INFORMATION

Haploclusters – Detect Excess Haplotypes Sharing

Haploclusters

:: DESCRIPTION

HAPLOCLUSTERS is a program designed to detect excess haplotypes sharing in datasets consisting of case and control haplotypes. Excess haplotype sharing can be seen around disease loci in case samples since LD persists longer here than in the controls where LD is persisting only according to the relatedness of the individuals in the population, i.e. the age of the population. This LD is often referred to as background LD.

::DEVELOPER

Melanie Bahlo (bahlo@wehi.edu.au) @ WEHI Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 Haploclusters

:: MORE INFORMATION

Citation:

Bahlo M, Stankovich J, Speed TP, Rubio JP, Burfoot RK, Foote SJ.
Detecting genome wide haplotype sharing using SNP or microsatellite haplotype data.
Hum Genet. 2006 Mar;119(1-2):38-50.

TreeScan 1.0 – Genotype-phenotype Associations from Haplotype Trees

TreeScan 1.0

:: DESCRIPTION

TREESCAN is intended to provide p-values for the hypothesis of association between evolutionary clades and continuous traits, using haplotype trees.

::DEVELOPER

Phylogenomics Group at the University of Vigo

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / MacOsX / Linux

:: DOWNLOAD

 TreeScan

:: MORE INFORMATION

Citation:

Posada D, Maxwell TJ, Templeton AR.
TreeScan: a bioinformatic application to search for genotype/phenotype associations using haplotype trees.
Bioinformatics 2005 21 (9): 2130-2132.doi: 10.1093/bioinformatics/bti29

HaploPowerCalc 1.0 – Haplotype Estimation

HaploPowerCalc 1.0

:: DESCRIPTION

HaploPowerCalc is a tool for estimating power to detect disease association by a set of markers (e.g. a tag SNP panel or SNPs on an array), at any user-specified polymorphic site(s), under arbitrary disease model and sample sizes. It is intended for users who wish to estimate the power (or sample sizes required to obtain adequate power) in their association study. HaploPowerCalc uses an approach based on haplotype-sampling.

::DEVELOPER

Dr. Deborah Nickerson’s lab at the University of Washington

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PHASE

:: DOWNLOAD

HaploPowerCalc

:: MORE INFORMATION

N/A