HaploBlockFinder

HaploBlockFinder V0.7

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 web-based utility for the analysis of haplotype blocks based on a greedy algorithm.

Accepted haplotype files format : FASTA (locus information file), Merlin, Arlequin, PHASE (both v1.0 and v2.0);
Results: A zip file containg several reports. (After pressing the Go button, please save the result with ".zip" as extension name, and open the compress file with Winzip or other similar programs);
Please refer to this simple documentation or the Bioinformatics paper (Zhang K and Jin L, Bioinformatics (2003) 19:1300-1301) if you wish to understand more about this program.
The source code is available for download.

Since you are here, you may want to take a quick look at another program Genotype2LDBlock I wrote that identifies LD blocks based on genotypes instead of haplotypes. This program may help you to compare how the local LD pattern is affected by the methods used.

Load haplotype file.		Load locus information file (OPTIONAL)

Parameters
Block definition	Threshold for LD measurement	Minimal chromosomal coverage
Filter options
Genotype quality filter	Minor allele frequency upper bound	Minor allele frequency lower bound
Options for the haplotype block diagram
Background	Color Map	Display mode
Show LD matrix (OPTIONAL, could be slow for a large number of loci)	Get tagging SNPs (OPTIONAL, could be slow for some large blocks)	Coverage of htSNPs
YesNo	YesNo
Options for the LD matrix diagram
LD Statistics (Top right)	LD Statistics (Bottom left)