Software
| Software | Short Description | Module name |
|---|---|---|
| Beast | Bayesian MCMC analysis of molecular sequences | module load beast |
| Eigensoft | Population structure analysis in genetic association | module load eigensoft |
| Eigensoft | Population structure analysis in genetic association | module load eigensoft |
| EMMAX | Mixed model association | module load emmax |
| Gasp | Genometric Analysis Simulation Program | module load gasp |
| Gassoc | Statistical methods for genetic associations | module load gassoc |
| GCTA | Estimating proportion of phenotypic variance explained by whole genome data | module load gcta |
| Genehunter | Linkage and disequilibrium analyses. | module load gh |
| GTool | Transforming sets of genotype data for use with the programs SNPTEST and IMPUTE | module load gtool |
| Impute | Imputation of unobserved genotypes in genome-wide case-control studies based on a set of known haplotypes | module load impute |
| Loki | Linkage analysis | module load loki |
| MACH | Markov Chain based haplotyper. It can be resolve long haplotypes or infer missing genotypes in samples of unrelated individuals | module load mach |
| MACH2qtl | can be used to analyse dosage information after mach imputation for quantitative traits | module load mach |
| MACH2dat | can be used to analyse dosage information after mach imputation for binary traits | module load mach |
| MAOS | Meta-analysis | module load maos |
| Mapmaker | Linkage analysis | module load mapmaker |
| Mega2 | Manipulation Environment for Genetic Analyses | module load mega2 |
| Mendel | Exact Statistical Analysis of Qualitative and Quantitative Traits. | module load mendel |
| Merlin | Pedigree analysis | module load merlin |
| METAL | meta-analysis of large datasets (such as several whole genome scans) in a convenient, rapid and memory efficient manner | module load metal |
| Mev | A microarray data analysis tool. | module load mev |
| MQLS | case-control association testing with related individals using genotype or allele dosage data | module load mqls |
| Mx | Matrix algebra interpreter and a numerical optimizer | module load mx |
| Openbugs | Bayesian inference Using Gibbs Sampling | module load openbugs |
| Pedig | Analysis of large populations | module load pedig |
| Plink | Whole Genome Association Analysis | module load plink |
| Plink-multivariate | Whole Genome Association Analysis for multivariate traits | module load plink-multivariate |
| Probabel | GWA analysis of imputed data | module load probabel |
| Qtdt | Linkage Disequilibrium Analyses for Quantitative and Discrete Traits | module load qtdt |
| R | Statistical computing | Available as is, no module command needed |
| Sage | Analyze pedigree data | module load sage |
| Simwalk | Statistical genetics computer application | module load simwalk |
| SNPtest | Analysis of single SNP association in genome-wide studies | module load snptest |
| Solar | Sequential oligogenic linkage analysis routines | module load solar |
| Transmit | Tests for association between genetic marker and disease | module load transmit |
| Twinsim | Twin analysis | module load twinsim |
| Unphased | Genetic association analysis | module load unphased |
| Vitesse | Multilocus linkage analysis via genotype set-recoding and fuzzy inheritance | module load vitesse |
If you want to use one of the following packages you need to state >module load [package].