A method and program for estimating graphical models for linkage disequilibrium that scale linearly with the number of loci, and their application to gene drop simulation.
BACKGROUND
Efficient models for genetic linkage disequilibrium (LD) are needed to enable appropriate statistical analysis of the dense, genome-wide single nucleotide polymorphism assays currently available.


RESULTS
Estimation of graphical models for LD within a restricted class of decomposable models is shown to be possible using computer time and storage that scale linearly with the number of loci. Programs for estimation and for simulating from these models on a whole-genome basis are described and provided.


BACKGROUND
Java classes and source code for IntervalLD and GeneDrops are freely available over the internet at http://bioinformatics.med.utah.edu/~alun.
Thomas
Alun
A
Department of Biomedical Informatics, Division of Genetic Epidemiology, University of Utah, 391 Chipeta Way Suite D, Salt Lake City, UT 84108, USA. alun@genepi.med.utah.edu
D002874:Chromosome Mapping; D019295:Computational Biology / Q000379:methods*; D020407:Internet; D015810:Linkage Disequilibrium; D008957:Models, Genetic; D020641:Polymorphism, Single Nucleotide; D011381:Programming Languages