HAPSIMU 1.0 – Genetic Simulation Platform based on real Haplotype Data

HAPSIMU 1.0

:: DESCRIPTION

HAPSIMU is based on real haplotype data from the HapMap ENCODE project. This platform can simulate heterogeneous populations with various known and controllable structures under the continuous migration model or the discrete model. Moreover, both qualitative and quantitative traits can be simulated using additive genetic model with various genetic parameters designated by users.

::DEVELOPER

Feng Zhang, Jianfeng Liu, Jie Chen and Hong-Wen Deng

:: SCREENSHOTS

:: REQUIREMENTS

Windows

:: DOWNLOAD

HAPSIMU

:: MORE INFORMATION

Citation

Zhang, Liu, Chen, Deng (2008),
“HAPSIMU: a genetic simulation platform for population-based association studies“,
BMC Bioinformatics, 9:331.

HaploVisual 0.04 – Haplotype data Visualization and Analyzation

HaploVisual 0.04

:: DESCRIPTION

The HaploVisual is a Java applet for haplotype data visualization and analyzation. It is intended to be used by both computer scientists (bioinformatics researchers) and biologists.

::DEVELOPER

Pasi Rastas

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux /MacOsX
Java

:: DOWNLOAD

HaploVisual

:: MORE INFORMATION

Citation

Ukkonen (2002),
“Finding founder sequences from a set of recombinants”
Lecture Notes in Computer Science Vol 2452, pp.277-286

HPM / TreeDT – Association Analysis using Haplotype data or Genotype data

HPM / TreeDT

:: DESCRIPTION

HPM (Haplotype Pattern Mining) is a program for gene mapping in case-control haplotype data.

TreeDT (Tree Disequilibrium Test) extracts, essentially in the form of substrings and prefix trees, information about historical recombinations in the population.

::DEVELOPER

Group of Data mining in genetics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux /MacOsX
C Compiler

:: DOWNLOAD

HPM / TreeDT

:: MORE INFORMATION

Citation

Hannu T. T. Toivonen et al,
Data mining applied to linkage disequilibrium mapping
Am J Hum Genet. 2000 July; 67(1): 133–145.

Sevon et al.
TreeDT: Tree pattern mining for gene mapping”
IEEE/ACM Trans Comput Biol Bioinform. 2006 Apr-Jun;3(2):174-85.