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ancestrymap
ANCESTRYMAP screens through the genome in a recently mixed population
such as African Americans, searching for segments with increased
ancestry from one of the ancestral populations, which can indicate the
position of disease genes
eigensoft
The EIGENSOFT package combines functionality from our population
genetics methods (Patterson et al. 2006) and our EIGENSTRAT
stratification method (Price et al. 2006). The EIGENSTRAT method uses
principal components analysis to explicitly model ancestry differences
between cases and controls along continuous axes of variation; the
resulting correction is specific to a candidate marker's variation in
frequency across ancestral populations, minimizing spurious associations
while maximizing power to detect true associations.
fbat
FBAT implements a broad class of Family Based Association Tests,
adjusted for population admixture.
metal
The METAL software is designed to facilitate meta-analysis of large
datasets (such as several whole genome scans) in a convenient, rapid and
memory efficient manner.
haploview
Haploview computes single locus and multi-marker haplotype
association tests. Haploview provides a framework for permuting your
association results in order to obtain a measure of
significance corrected for multiple testing bias.
impute
IMPUTE is a program for estimating ("imputing") unobserved genotypes in
SNP association studies.
merlin
MERLIN uses sparse trees to represent gene flow in pedigrees and is one
of the fastest pedigree analysis packages around.
plink
PLINK is a free, open-source whole genome association analysis toolset,
designed to perform a range of basic, large-scale analyses in a
computationally efficient manner.
The focus of PLINK is purely on analysis of genotype/phenotype data, so
there is no support for steps prior to this (e.g. study design and
planning, generating genotype or CNV calls from raw data). Through
integration with gPLINK and Haploview, there is some support for the
subsequent visualization, annotation and storage of results.
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solar
SOLAR is an extensive, flexible software package for genetic variance
components analysis, including linkage analysis, quantitative genetic
analysis, SNP association analysis (QTN and QTLD), and covariate
screening. Operations are included for calculation of marker-specific or
multipoint identity-by-descent (IBD) matrices in pedigrees of arbitrary
size and complexity, and for linkage analysis of multiple quantitative
traits and/or discrete traits which may involve multiple loci
(oligogenic analysis), dominance effects, household effects, and
interactions.
MACH
MACH is a Markov Chain based haplotyper. It can resolve long haplotypes or infer missing genotypes in samples of unrelated individuals.
Beagle
BEAGLE is a state of the art software package for analysis of large-scale genetic data sets with hundreds of thousands of markers genotyped on thousands of samples. This software is not installed system-wide, as it does not require such. Instead download it by using the following command: wget http://www.stat.auckland.ac.nz/~bbrowning/beagle/beagle.jar
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