Instructions for running program for 'Haplotype Blocks':
Overview
The Human Genome consists of regions having limited Haplotype Diversity. These regions are described as "blocked" and known as "Haplotype Blocks". The algorithm developed aims to identify those regions which exhibit substantial multi-locus disequilibrium and range over a greater number of SNPs. This method allows one or more SNPs to separate blocked regions or for adacent blocks. The model used computes the likelihood of the data minus a penalty for model complexity. This model is based upon the usual criteria for blocks: the resulting blocks have very low diversity and the linkage disequilibrium with SNP's outside the blocks is low.
The main program (Entropy_blocker.txt) is implemented in the R programming language (freeware version of S-Plus) for Windows and Linux (version 1.7.0). Thus, the first step in running the program will be to download a copy of R if you do not already have it installed. To download R, go to
and follow the necessary links to download R for Windows/Linux.
Once R is installed, simply type R at the command prompt to start. To quit R, type q() at the R command prompt. To cancel an R command, type control-c.
Instructions and Description of Output
Example File 1
Sample Input File (Haplotypes with 0 and 1 alleles)
Example File 2 (Gene il21r from http://pga.mbt.washington.edu)
Sample Input File (Complete PHASE output)
Sample Input File (Using -T option in PHASE, Please see instructions)
