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 |