Bioinformatics Group @ IPM
PapreHapHelp
Partially Perfect Haplotype Block Partitioning
Here you can obtain a block partitioning for any haplotype matrix with your own parameters.
1.Upload file:
You should enter your file address.Your file should include a haplotype matrix that each row represents a haplotype and each column represents a SNP position. Between any two SNPs you may have any specific constant number of spaces. The entries may be a,c,g and t,or 0 and 1. It is possible to include missing data. In this case you need to enter its character in the proper place. (Example)
2.The character to be used for missing data:
If your file includes any missing data, you need to specify them by assigning a character to them.
3.The percentage of common haplotypes in each block:
You should determine the minimum percentage of common haplotypes in each block.
4.The perfect percentage of each block:
You should enter a number k, so that in each block by changeing at most (100-k)% of entries the block it becomes a perfect one.
5.The percentage of pattern which is covered by tag SNPs:
You should enter a number k, so that for each block at least k% of its patterns (haplotypes) could be recognized by our tag SNPs.