Genetic Cluster Computer


SoftwareShort DescriptionModule name
BeastBayesian MCMC analysis of molecular sequencesmodule load beast
EigensoftPopulation structure analysis in genetic associationmodule load eigensoft
EigensoftPopulation structure analysis in genetic associationmodule load eigensoft
EMMAXMixed model associationmodule load emmax
GaspGenometric Analysis Simulation Programmodule load gasp
GassocStatistical methods for genetic associationsmodule load gassoc
GCTAEstimating proportion of phenotypic variance explained by whole genome datamodule load gcta
GenehunterLinkage and disequilibrium analyses.module load gh
GToolTransforming sets of genotype data for use with the programs SNPTEST and IMPUTEmodule load gtool
ImputeImputation of unobserved genotypes in genome-wide case-control studies based on a set of known haplotypesmodule load impute
LokiLinkage analysismodule load loki
MACHMarkov Chain based haplotyper. It can be resolve long haplotypes or infer missing genotypes in samples of unrelated individualsmodule load mach
MACH2qtlcan be used to analyse dosage information after mach imputation for quantitative traitsmodule load mach
MACH2datcan be used to analyse dosage information after mach imputation for binary traitsmodule load mach
MAOSMeta-analysismodule load maos
MapmakerLinkage analysismodule load mapmaker
Mega2Manipulation Environment for Genetic Analysesmodule load mega2
MendelExact Statistical Analysis of Qualitative and Quantitative Traits.module load mendel
MerlinPedigree analysismodule load merlin
METALmeta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient mannermodule load metal
MevA microarray data analysis tool.module load mev
MQLScase-control association testing with related individals using genotype or allele dosage datamodule load mqls
MxMatrix algebra interpreter and a numerical optimizermodule load mx
OpenbugsBayesian inference Using Gibbs Samplingmodule load openbugs
PedigAnalysis of large populationsmodule load pedig
PlinkWhole Genome Association Analysismodule load plink
Plink-multivariateWhole Genome Association Analysis for multivariate traitsmodule load plink-multivariate
ProbabelGWA analysis of imputed datamodule load probabel
QtdtLinkage Disequilibrium Analyses for Quantitative and Discrete Traitsmodule load qtdt
RStatistical computingAvailable as is, no module command needed
SageAnalyze pedigree datamodule load sage
SimwalkStatistical genetics computer applicationmodule load simwalk
SNPtestAnalysis of single SNP association in genome-wide studiesmodule load snptest
SolarSequential oligogenic linkage analysis routinesmodule load solar
TransmitTests for association between genetic marker and diseasemodule load transmit
TwinsimTwin analysismodule load twinsim
UnphasedGenetic association analysismodule load unphased
VitesseMultilocus linkage analysis via genotype set-recoding and fuzzy inheritancemodule load vitesse

If you want to use one of the following packages you need to state >module load [package].