MDBLOCKS 1.0 – Minimum Description length method for Haplotype BLOCKS

MDBLOCKS 1.0

:: DESCRIPTION

MDBLOCKS( Minimum Description length method for Haplotype BLOCKS) uses the mimimum description length model to delineate haplotype blocks.

::DEVELOPER

Eric C. Anderson and John Novembre

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 MDBLOCKS

:: MORE INFORMATION

Citation:

Anderson, Novembre (2003),
Finding haplotype block boundaries by using the minimum description length criterion“,
American Journal of Human Genetics, 73(2):336-354

HaploBlock 1.2 – Haplotype Block Identification and Resolution for High-density SNP data.

HaploBlock 1.2

:: DESCRIPTION

HaploBlock is a software program which provides an integrated approach to haplotype block identification, haplotyping SNPs (or haplotype phasing, resolution or reconstruction) and linkage disequilibrium (LD) mapping (or genetic association studies). HaploBlock is suitable for high density haplotype or genotype SNP marker data and is based on a statistical model which takes account of recombination hotspots, bottlenecks, genetic drift and mutations and has a Markov Chain at its core.

::DEVELOPER

Laboratory of Computational Biology , Technion

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux / Mac OsX

:: DOWNLOAD

 HaploBlock

:: MORE INFORMATION

Citation

G. Greenspan* and D. Geiger
High Density Linkage Disequilibrium Mapping using Models of Haplotype Block Variation
Bioinformatics (2004) 20 (suppl 1): i137-i144.

HapFinder 1.0 – Finding common Haplotype Blocks in a database

HapFinder 1.0

:: DESCRIPTION

HapFinder is a method which can find the common longest haplotype under three different settings from a database, which is relevant in the analysis of positive selection in population genetics and also in medical genetics for finding the likely haplotype form carrying the causal allele at the functional polymorphism.

::DEVELOPER

Singapore Genome Variation Project

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R package
  • Java

:: DOWNLOAD

 HapFinder

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Mar 15;27(6):822-8. doi: 10.1093/bioinformatics/btr007. Epub 2011 Jan 6.
A method for identifying haplotypes carrying the causative allele in positive natural selection and genome-wide association studies.
Ong RT, Liu X, Poh WT, Sim X, Chia KS, Teo YY.

MDLBlockFinder 1.1 – Haplotype Block Identification

MDLBlockFinder 1.1

:: DESCRIPTION

MDLBlockFinder is a software package for the analysis of haplotype block structures.

::DEVELOPER

Mikko Koivisto

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / UNIX

:: DOWNLOAD

  MDLBlockFinder

:: MORE INFORMATION