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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.

NameWhat it does
BP2CM Replace bp by map positions in PLINK map files
EH Estimate LD (linkage disequilibrium) for 2 or more loci
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
MAXSTATDEL Detecting pathogenic deletions using Hamming distance
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
PAWE/3D PAWE/3D programs taken unmodified from previous lab server
PropHet Heterozygosity Analysis for dominant genes (under construction)
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
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
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

 

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 prog