Access programs by name

Some programs have had their names changed and/or been superseded by new programs. Go here for a list.

ApproxGCHap This program finds approximations to the maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals.

CheckErrors This program finds the posterior probabilities of errors for genotypes on individuals in pedigrees given a set of observed genotypes and the pedigree structure.

CheckFormat This program reads in LINKAGE parameter and pedigree files, checks that they are readable and then outputs the checked files.

CheckParameters This program reads in a LINKAGE parameter, checks that it is correctly foratted and then outputs the checked file.

CheckPedigree This program reads in LINKAGE a pedigree file, and checks that the pedigree information is correctly formatted and self consistent.

CheckTriplets This program checks a pedigree specified by a list of triplets for self consistency and completeness.

Complete This program takes genotype data, specified as LINKAGE parameter and pedigree files, and either imputes or samples complete phase known hapolotype data, using a specified graphical model for linkage disequilibrium.

DownCodeAlleles This program reduces the number of alleles in the models for the given genetic loci to include only alleles that appear in the pedigree file plus, optionally, one catchall allele to represent the unseen alleles which has frequency equal to the total frequency of the original unseen alleles.

FitGM This program estimates a graphical model for discrete multivariate data.

FitGMLD This program estimates a graphical model for linkage disequilibrium from a data set assumed to contain a population sample of genotyped individuals.

FitIntervalLD This program estimates a graphical model for linkage disequilibrium from a data set assumed to contain a population sample of genotyped individuals.

GCHap This program finds maximum likelihood estimates of haplotype frequencies from a sample of genotyped individuals.

GeneCountAlleles This program calculates maximum likelihood estimates of allele frequencies from genotypes observed in individuals related in pedigrees.

GeneDrop This program uses the multi locus gene drop method to simulate genotypes on a pedigree to match those in the input.

GeneDrops This program uses the multi locus gene drop method to simulate genotypes on a pedigree to match those in the input.

GetPolymorphisms This program selects from the input data the marker loci for which at least two alleles are observed.

HGS This program calculates the runs of loci at which the selected individuals are all homozygous, but not necessarily for the same allele.

HapMapToLinkage This converts a file of maker information in the format used by the HapMap project into standard LINKAGE parameter and pedigree files.

HetCutOff This program selects from the input data the marker loci for which the heterozygosity score is higher than a given threshold.

HetLods This program calculates two point Hetlod scores on a grid of points.

Heterozygosities This program reads in a LINKAGE parameter, and outputs the heterozygosity measure for each locus.

HomozygousSGS This program calculates the runs of homozygous sharing for a set of individuals in a pedigree.

LinkageToFastPhase Takes data from LINKAGE format parameter and pedigree files and prepares it for input into the FASTPHASE haplotyping program.

LinkageToPhase Takes data from LINKAGE format parameter and pedigree files and prepares it for input into the PHASE haplotyping program.

LocusLogLikelihoods This program calculates the log likelihood for the data for each pedigree at each locus specified in the input.

MakePed This program reads converts a pedigree file in "premakeped" format into a standard LINKAGE pedigree file.

MakeProbands This programs marks individuals in a pedigree file as being or not being probands.

MaxTwoPointLods This program finds the maximum two point Lod scores for values of the recombination between 0 and 0.5 and between 0.5 and 1.

McCheck This program uses Markov chain Monte Carlo methods for fully informative multi locus error detection for linked loci in a pedigree.

McKinship This program samples the posterior distribution of inheritance vectors given the observed genotypes and, hence, estimates posterior probabilities of kinship.

McLinkage The programs combines McMultiPoints and McTLods to give both true multi point Lod scores and Tlod statistics.

McMultiPoints This program samples the posterior distribution of inheritance vectors given the observed genotypes and, hence, calculated multi point Lod scores between a trait phenotype and genetic markers in pedigrees.

McTLods This program samples the posterior distribution of inheritance vectors given the observed genotypes and, hence, calculates Tlod linkage statistics between a trait phenotype and genetic markers in pedigrees.

ObligateErrors This program checks genotype data on pedigrees and indicates whether the data at any particular locus is inconsistent with Mendelian inheritance.

SGS This program calculates the runs of heterozygous sharing for a set of individuals in a pedigree. The individuals to consider are specified by having a 1 in the proband field of the input LINKAGE pedigree file.

SelectKindreds This program selects a subset of kindreds from a LINKAGE pedigree file.

SelectLoci This program selects a subset of loci from LINKAGE parameter and pedigree files.

SelectPedigrees Another name for the SelectKindreds program.

SimHGS This program performs multi locus gene drop simulations in order to assess the distribution of the length of regions of homozygosity, as calculated by HGS.

SimHomozygousSGS This program performs multi locus gene drop simulations in order to assess the distribution of the length of homozygously shared genomic regions, as calculated by HomozygousSGS.

SimSGS This program performs multi locus gene drop simulations in order to assess the distribution of the length of heterozygously shared genomic regions, as calculated by SGS.

Triangulate This program uses a greedy algorithm to find a triangulation of the input graph.

TrimPed This program removes individuals from the pedigree unless they have a minimum number of loci at least partially observed or they are ancestors of someone else that is observed.

TwoPointLods This program calculates two point Lod scores on a grid of points.

ViewDAG This is and interactive graphical program for viewing and editing a directed acyclic graph.

ViewGraph This is and interactive graphical program for viewing and editing a graph.

ViewLinkPed This is an interactive graphical program for viewing pedigree data.

ViewPed This is an interactive graphical program for viewing pedigree data.

ZeroLoopPed This program generates random zero loop pedigrees with specified numbers of marriages and individuals and converts these to recombination fractions.

cMorgansToTheta This program reads in a LINKAGE parameter file assuming that the distances between the loci are specified as cMorgans.