HIPPO 1.0/ AEML 1.0 – Estimate Population Haplotype Frequencies from Pooled SNP data

HIPPO 1.0/ AEML 1.0

:: DESCRIPTION

Hippo (Haplotype estimation under incomplete prior information using pooled observations) is a program for estimating haplotype distribution from pooled DNA data and is able to utilize prior information about the haplotypes that are known to be present in the population.

AEML is a program for estimating haplotype distribution from pooled DNA data and is able to utilize prior information about the haplotypes that are known to be present in the population.

::DEVELOPER

Matti Pirinen

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux
GCC

:: DOWNLOAD

HIPPO – AEML Source Code

:: MORE INFORMATION

Citation

Matti Pirinen
Estimating population haplotype frequencies from pooled SNP data using incomplete database information
Bioinformatics (2009) 25 (24): 3296-3302

GSA-SNP 20130719 – Process SNP data as well as Gene and Haplotype data

GSA-SNP 20130719

:: DESCRIPTION

GSA-SNP is a gene set analysis software that can process SNP data as well as gene and haplotype data.

::DEVELOPER

Dr. Dougu Nam , Dr. Sangsoo Kim

:: SCREENSHOTS

:: REQUIREMENTS

Linux / Windows/ MacOsX
Java

:: DOWNLOAD

GSA-SNP

:: MORE INFORMATION

Citation

GSA-SNP: a general approach for gene set analysis of polymorphisms.
Nam D, Kim J, Kim SY, Kim S.
Nucleic Acids Res. 2010 Jul;38(Web Server issue):W749-54. doi: 10.1093/nar/gkq428. Epub 2010 May 25.

trueFS – Find Ascertainment Corrected Frequency Spectrum based on Ascertained SNP data

trueFS

:: DESCRIPTION

trueFS is a program used for finding the ascertainment corrected frequency spectrum based on ascertained SNP data. It can perform the corrections under multiple different models including double-hit ascertainment models and ascertainment with or without overlap between the original ascertainment sample and the final genotyped sample. It uses a bootstrap method to quantify statistical uncertainty in the estimates

::DEVELOPER

the Nielsen group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows / Linux
C Compiler

:: DOWNLOAD

trueFS

:: MORE INFORMATION

Citation:

Nielsen, R., M. J. Hubisz and A. G. Clark. 2004.
Reconstituting the frequency spectrum of ascertained SNP data.
Genetics 168: 2373-2382.

SweepFinder 20060814 – Detect the Location of a selective Sweep based on SNP data

SweepFinder 20060814

:: DESCRIPTION

SweepFinder is a program used to detect the location of a selective sweep based on SNP data. It will also estimate the frequency spectrum of observed SNP data in the presence of missing data.

::DEVELOPER

the Nielsen group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX

:: DOWNLOAD

SweepFinder

:: MORE INFORMATION

Citation:

Nielsen et al. 2005.
Genomic scans for selective sweeps using SNP data.
Genome Research 1566-1575.

MAGprediction – Gene Allele Prediction Using Unphased SNP data

MAGprediction

:: DESCRIPTION

MAGprediction (Multi-allelic Gene Prediction) is a software which was developed for predicting highly polymorphic gene alleles using unphased SNP data.

::DEVELOPER

Fred Hutchinson Cancer Research Center

:: SCREENSHOTS

:: REQUIREMENTS

Windows / Linux
Matlab

:: DOWNLOAD

MAGprediction

:: MORE INFORMATION

Citation

Li SS, Wang H, Smith A, Zhang B, Zhang XC, Schoch G, Geraghty D, Hansen JA, Zhao LP
Predicting Highly Polymorphic Alleles Using Unphased and Flanking Single Nucleotide Polymorphisms.
Genetic Epidemiology 2011,35(2):85-92

Overpaint 0.2 – Joint Estimation of Gene Conversion Rates and Mean Conversion Tract Lengths from Population SNP data

Overpaint 0.2

:: DESCRIPTION

Overpaint is a C++ package that can jointly estimate crossover rates, gene conversion rates and mean conversion tract lengths from population SNP dataset.

::DEVELOPER

Yun S. Song

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux /MacOsX
gsl

:: DOWNLOAD

Overpaint

:: MORE INFORMATION

Citation

Yin, J. Jordan, M. I., and Song, Y. S..
Joint estimation of gene conversion rates and mean conversion tract lengths from population SNP data,
Bioinformatics, 25 (2009) i231-i239