Sweep

Record added by Jurg Ott (the original Rockefeller list)

December 2005

SWEEP allows large-scale analysis of haplotype structure in genomes for the primary purpose of detecting evidence of natural selection. Primarily, it uses the Long Range Haplotype test to look for alleles of high frequency with long-range linkage disequilibrium, which suggest the haplotype rapidly rose to high frequency before recombination could break down associations with nearby markers. SWEEP takes phased genotype data as input, detects all haplotype blocks in that data, and then determines the frequency and long-range LD for each allele in each block.

• Patrick Varilly
• Ben Fry
• Oleg Shamovsky
• Pardis Sabeti (email: sweep@broad.mit.edu)

http://www.broad.mit.edu/mpg/sweep/

Sabeti, Reich, Higgins, Levine, Richter, Schaffner, Gabriel, Platko, Patterson, McDonald, Ackerman, Campbell, Altshuler, Cooper, Kwiatkowski, Ward, Lander (2002), “Detecting recent positive selection in the human genome from haplotype structure”, Nature, 419:832-827.