Haplotype Estimation and Linkage Disequilibrium Methods Manual: Version 0.1.8 (June 3, 2011) Estimating Haplotype Frequencies and Linkage Disequilibrium Parameters in the HLA and KIR Regions Available online at: www.ImmPort.org

1 Department of Mathematics and Statistics, 306 Mansfield House, University of Vermont, Burlington, VT 05405, USA, [email protected] 2 Department of Neurology, 513 Parnassus Avenue, University of California, San Francisco, CA 94143-0436, USA, e-mail: [email protected] 3 Department of Integrative Biology, 3060 Valley Life Sciences Building MC #3140, University of California, Berkeley, CA 94720-3140, USA, e-mails: [email protected], [email protected] 4 Mailing address: Whitehead Institute for Biomedical Research, Nine Cambridge Center, Cambridge, MA 02142, USA 5 Division of Epidemiology, School of Public Health, University of California, Berkeley, CA 94720-, USA, e-mails: [email protected], [email protected] 6 Center for Genetics, Children's Hospital Oakland Research Institute, 5700 Martin Luther King Jr Way, Oakland, CA 94609, USA, e-mails: [email protected], [email protected]