title: LdCompare: rapid computation of single- and multiple-marker r2 and genetic coverage.
abstract: The scale of genetic-variation datasets has increased enormously and the linkage equilibrium (LD) structure of these polymorphisms, particularly in whole-genome association studies, is of great interest. The significant computational complexity of calculating single- and multiple-marker correlations at a genome-wide scale remains challenging. We have developed a program that efficiently characterizes whole-genome LD structure on large number of SNPs in terms of single- and multiple-marker correlations.
  
  
  BACKGROUND
  LdCompare is licensed under the GNU General Public License (GPL). Source code, documentation, testing datasets and precompiled executables are available for download at: http://www.affymetrix.com/support/developer/tools/devnettools.affx
authors.affiliation: Algorithm and Data Analysis, Affymetrix Inc. 3420 Central Expressway, Santa Clara, California, USA. ke_hao@affymetrix.com
authors.forename: K
authors.initials: K
authors.lastname: Hao
authors.forename: X
authors.initials: X
authors.lastname: Di
authors.forename: S
authors.initials: S
authors.lastname: Cawley
mesh_terms: D000465:Algorithms; D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D005819:Genetic Markers / Q000235:genetics*; D014644:Genetic Variation / Q000235:genetics; D015810:Linkage Disequilibrium / Q000235:genetics*; D008969:Molecular Sequence Data; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013223:Statistics as Topic
chemical_list: D005819:Genetic Markers