haplotypes. This measure is suitable only for haplotype blocks with limited haplotype diversity and it is not clear how to use it for large data sets consisting of multiple haplotype blocks. Some recent works evaluate tag SNPs selection algorithms based on how well the tagging SNPs can be used to predict non-tagging SNPs. The prediction accuracy is determined using cross-validation such as leave-one-out or hold out. In leave-one-out cross-validation, for each sequence in the data set, the algorithm is run on the rest of the data set to select a minimum set of tagging SNPs. Tools Tagger Tagger is a web tool available for evaluating and selecting tag SNPs from genotypic data such as the International HapMap Project. It utilizes pairwise methods and multimarker haplotype approaches. Users can upload HapMap genotype data or pedigree format and the linkage disequilibrium patterns will be calculated. Tagger options allow for the user to specify chromosomal landmarks, which indicate regions of interest in the genome for picking tag SNPs. The program then produces a list of tag SNPs and their statistical test values as well as a coverage report. It is developed by Paul de Bakker in the labs of David Altshuler and Mark Daly at the Center for Human Genetic Research of Massachusetts General Hospital and Harvard Medical School, at the Broad Institute. CLUSTAG and WCLUSTAG In the freeware CLUSTAG and WCLUSTAG, there contain cluster and set-cover algorithms to obtain a set of tag SNPs that can represent all the known SNPs in a chromosomal region. The programs are implemented with Java, and they can run in Windows platform as well as the Unix environment. They are developed by SIO-IONG AO et al. in The University of Hong Kong. See also International HapMap Project Genome-wide association study Single Nucleotide Polymorphism Linkage disequilibrium References Genetic polymorphisms Genomics Population genetics