MIXMUL – Estimating Haplotype Frequencies and Reconstructing Haplotypes from Mixed Genotype Data

MIXMUL

:: DESCRIPTION

MIXMUL (Mixture of Weighted Multinomial) procedure is a convenient haplotype inference tool for mixed data to estimate haplotype frequencies accurately and output the most likely reconstructed haplotype pairs of each subject in the estimation.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R package

:: DOWNLOAD

 MIXMUL

:: MORE INFORMATION

Citation

J Biomed Sci. 2009 Jun 2;16:52. doi: 10.1186/1423-0127-16-52.
A novel tool for individual haplotype inference using mixed data.
Lin CP, Fann CS.

Batman – Bayesian Tool for Methylation Analysis

Batman

:: DESCRIPTION

Batman is a new tool for analysing DNA methylation data from MeDIP experiments combined with microarray or high-throughput sequencing assays.

::DEVELOPER

Thomas Down

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 Batman

:: MORE INFORMATION

Citation:

Thomas A Down et al.
A Bayesian deconvolution strategy for immunoprecipitation-based DNA methylome analysis
Nature Biotechnology 26, 779 – 785 (2008)

HapMDR – Detection of Haplotype-haplotype Interaction

HapMDR

:: DESCRIPTION

HapMDR is a convenient analysis tool for detecting disease-related haplotype-haplotype interactions. HapMDR overcome high-dimensional issues which combine the advantages of data mining with the concept of haplotypes and consider haplotype uncertainty.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R package

:: DOWNLOAD

 HapMDR

:: MORE INFORMATION

hapCART – Detect Interactions among Haplotypes in Association with a Disease

hapCART

:: DESCRIPTION

HapCART is a convenient analysis tool for detecting disease-related haplotype-haplotype interactions. HapCART overcome high-dimensional issues which combine the advantages of data mining with the concept of haplotypes and consider haplotype uncertainty.

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R package

:: DOWNLOAD

  HapCART

:: MORE INFORMATION

MSS v1 – Analysis of Genome-wide Association Data

MSS v1

:: DESCRIPTION

MSS (Maximal Segmental Score) is an R program for the analysis of genome-wide association data

::DEVELOPER

Cathy S.J. Fann lab,Institute of Biomedical Informatics, National Yang-Ming University, Taipei

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows
  • R package

:: DOWNLOAD

 MSS

:: MORE INFORMATION

Citation

Using maximal segmental score in genome-wide association studies.
Lin YC, Hsiao CL, Hsieh AR, Lian IeB, Fann CS.
Genet Epidemiol. 2012 Sep;36(6):594-601. doi: 10.1002/gepi.21652.

FaBox 1.61 – Online FASTA Sequences Toolbox

FaBox 1.61

:: DESCRIPTION

FaBox is a collection of simple and intuitive web services that enable biologists and medical researchers to quickly perform typical task with sequence data. The services makes it easy to extract, edit, and replace sequence headers and join or divide data sets based on header information. Other services include collapsing a set of sequences into haplotypes and automated formatting of input files for a number of population genetics programs, such as ARLEQUIN , TCS and MRBAYES . The toolbox is expected to grow on the basis of requests for particular services and converters in the future.

::DEVELOPER

Palle Villesen Fredsted

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/Windows/MacOsX
  • WebServer
  • PHP

:: DOWNLOAD

 FaBox

:: MORE INFORMATION

Citation

Villesen, P (2007),
FaBox: an online toolbox for fasta sequences,
Molecular Ecology Notes 7 (6), 965-968. doi:10.1111/j.1471-8286.2007.01821.x

MicroFamily 1.2 – Detect Flanking Region Similarities among different Microsatellite Loci

MicroFamily 1.2

:: DESCRIPTION

MicroFamily is a program designed for identifying flanking region similarities between different microsatellite sequences obtained from screening partial genomic libraries.

::DEVELOPER

Emese Meglécz

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 MicroFamily

:: MORE INFORMATION

Citation

Meglécz, E. 2007.
MicroFamily: A computer program for detecting flanking region similarities among different microsatellite loci.
Molecular Ecology Notes 7 : 18-20

Odefy 1.20 – From Discrete to Continuous Models

Odefy 1.20

:: DESCRIPTION

Odefy is a MATLAB- and Octave-compatible toolbox for the automated transformation of Boolean models into systems of ordinary differential equations.

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

Odefy

:: REQUIREMENTS

  • Windows / MacOsX/ Linux
  • Matlab / Octave

:: DOWNLOAD

 Odefy

:: MORE INFORMATION

Citation

Krumsiek J, Poelsterl S, Wittmann DM, Theis FJ.
Odefy – From discrete to continuous models.
BMC Bioinformatics. 2010, 11:233.

simbTUM 3.0a – Simulation of Stochastic processes and ODE models in Biology

simbTUM 3.0a

:: DESCRIPTION

simbTUM allows to define ODE-models or stochastic compartemental models of biological processes, to simulate, to fit data and to do some statistics (fitting and statistics for deterministic models only).

::DEVELOPER

Institute of Computational Biology, German Research Center for Environmental Health (GmbH)

:: SCREENSHOTS

simbTUM

:: REQUIREMENTS

  • Windows 

:: DOWNLOAD

 simbTUM

:: MORE INFORMATION

SeSiMCMC 4.36 – Dig For DNA Motifs Gibbs Sampler

SeSiMCMC 4.36

:: DESCRIPTION

The SeSiMCMC (Sequence Similarities by Markov Chain Monte Carlo) algorithm finds DNA motifs of unknown length and complicated structure, such as direct repeats or palindromes with variable spacers in the middle in a set of unaligned DNA sequences. It uses an improved motif length estimator and careful Bayesian analysis to consider site absence in a sequence.

::DEVELOPER

Alexander Favorov

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WIndows / Linux

:: DOWNLOAD

 SeSiMCMC

:: MORE INFORMATION

Citation:

A Gibbs sampler for identification of symmetrically structured, spaced DNA motifs with improved estimation of the signal length.
Favorov AV, Gelfand MS, Gerasimova AV, Ravcheev DA, Mironov AA, Makeev VJ.
Bioinformatics. 2005 May 15;21(10):2240-5. Epub 2005 Feb 22.