Notice: Because of the inconvenience for me to access this server, I have set up a mirror site at Harvard and all future modifications will be made on the Harvard site only! KZ @ 05/11/2005

This is a program that partitions LD blocks based on genotypes. It can handle thousands of loci at once. To do this, all pair-wise haplotypes are first inferred using the EM algorithm, and the LD matrix is calculated. LD blocks are then identified based on the pair-wise LD matrix using a greedy algorithm.

• Accepted genotype format: PHASE input format.For data in the Linkage format, here is a nice reformating tool you could use.
• Reports: A zip file containing (it might appear as a cgi file depending on the browser you use, in which case you need to save it explicitly as a zip file.):
• LDblock.txt: A text delimited file containing the basic information of the blocks;
• LDblock_diagram.png: A graphical diagram of the LD matrix and blocks;
• LDmatrix.txt: All pair-wise LD values (left-bottom: |D'|, top-right: r2);
• Files in the PHASE_genotypes directory: Genotypes for each blocks in the PHASE format, for haplotype inference using the PHASE program.
• Files in the SNPHAP_genotypes directory: Genotype for each block in the SNPHAP format, for haplotype inference using the SNPHAP program.
• A standalone version of this program is available upon request.