Software
Identity Coefficients: Compute the condensed identity coefficients for pairs of individuals (Kan Lange’s book Mathematical and Statistical Methods for Genetic Analysis [2002] has a good description of identity coefficients). This software uses novel algorithms I developed to be able to do the computations very efficiently and rapidly, even for very large and complex pedigrees.
The current version is idcoefs 2.1.
Download: Idcoefs2_1.tar.gz
IBD Estimation and Linkage: Estimate pairwise identity by descent (IBD) probabilities in very large pedigrees. This software can compute the proportion of alleles shared IBD between a pair of individuals at a marker given all genotypes at that marker and the entire, unbroken, pedigree. The method implemented here is particularly useful for pedigrees that are very deep and there are multiple generations with missing genotype data. This requires knowing the condensed identity coefficients of a subset of the individuals in the pedigree.
Genetic Analysis of Qualitative Traits: Estimate covariate effects and variance components for a binary trait. Here we use a generalized linear mixed model for the trait and use a Monte Carlo expectation maximization method to obtain maximum likelihood estimates of the model parameters. Our method can successfully analyze large samples (hundreds) of affected and unaffected individuals, all of whom may be related.
A more detailed description.
The current version will be made available soon!
Updated August 26, 2008