Computer Programs
The list below shows our main statistical genetics programs; click on names to download programs and manuals. More detailed information may be found on our general program webpage. The newer programs are available for Windows and Linux.
| Name | What it does |
|---|---|
| BP2CM | Replace bp by map positions in PLINK map files |
| EH | Estimate LD (linkage disequilibrium) for 2 or more loci |
| GPM | Find genotype patterns (gene-gene interaction) in case-control data |
| FPtest | Association test based on inbreeding coefficient |
| HOMOG | Linkage analysis with genetic heterogeneity |
| LINKAGE | Pedigree linkage analysis for Windows and Linux |
| LIPED | First-generation linkage analysis program, available for Windows and Linux |
| MAXSTAT | Permutation-based tests in GWAS |
| MAXSTATRS | Analysis of Hamming distance between sets of variants in two individuals |
| NOCOM | Estimating parameters for a mixture of distributions |
| P2S | Converting files from plink to sumstat format |
| PH | Heterozygosity Analysis for dominant disease variants |
| PTest | Partition test: Testing set of observed small p-values in GWAS |
| RANDOMPAT | Genotype pattern frequencies in case-control association mapping |
| SCANSTAT | Scan statistics for disease gene association of a set of contiguous SNPs |
| SHARED SEGMENTS | Determine significance of sharing a variant by multiple individuals |
| SIMNUCLEAR | Simulate affected and unaffected individuals in nuclear pedigrees |
| SIMULATE | Simulate genotypes in families unlinked to affection status |
| SLINK | General simulation program for linkage analysis |
| STATDEL | Detecting pathogenic deletions using Hamming distance |
| SUMSTAT | Sum statistics for multi-locus genetic association mapping |
| TDTae | TDT analysis (family-based association) allowing for genotyping errors |
| TLINKAGE | Two-locus linkage analysis |
| UTIL | Statistical genetics utility programs |
