Software for tag single nucleotide polymorphism selection

Table 1 Features of the tag single nucleotide polymorphism (SNP) programs evaluated

Program	Block-based?	Estimates blocks itself?	Reads HapMap data?	PLEM incorporates trio data?	Criteria for picking tag SNPs^a	Allows 'force in' of special SNPs	Platforms/require software
Haploview	YES	YES	YES	YES	Unknown	No	Java
Hapblock	YES	YES	NO	YES	Haplotype $R_{h}^{2}$ , pairwise R², information entropy	Yes	Compiled C program for Win/DOS Unix and Linux
LDSelect	NO	N/A	NO	N/A	Pairwise R²	YES	Perl
htSNP	YES	NO	NO	NO	Allelic $R_{s}^{2}$ , haplotype $R_{s}^{b}$	NO	Stata + compiled C program (SNPHAP)
TagIT	YES	NO	NO	YES^b	Allelic $R_{s}^{2}$ , haplotype $R_{s}^{2}$	YES	Matlab
Tagger	NO	N/A	YES	YES	Pairwise R², restricted haplotype $R_{s}^{2}$	YES	Web application
tagSNPs	YES	NO	YES	YES	Haplotype $R_{h}^{2}$ 2, haplotype $R_{s}^{2}$ , pairwise R²	YES	Compiled Fortran program for WIN/DOS Unix and Linux

^a See text for definition of notation.
^b Performs a standard EM rather than PLEM algorithm (see text for more information).

ISSN: 1479-7364