Thanks for your answer.

There's no information about how to compute haplotypes blocks on the HapMap tutorial page, it's a tutorial about how to use the web interface of the HapMap querier.

I understood what you told me and I started my development on that, now I "parse" [?]this[?] on [?]this other thing[?].

I still have no idea about how to do the math to get the LOD, R2, D' for example.

Thanks for your answer.

There's no information about how to compute haplotypes blocks on the HapMap tutorial page, it's a tutorial about how to use the web interface of the HapMap querier.

I understood what you told me and I started my development on that, now I "parse" http://hapmap.ncbi.nlm.nih.gov/cgi-perl/phased?chr=chr3&pop=CEU&start=200000&stop=250000&ds=pIII&out=txt&filter=cons to http://bioinf.cs.ipm.ir/gpmap/examples/sample.ped with what you told me.

I still have no idea about how to do the math to calculate the LOD, R2, D' for example.

Do I have to do something with allele freq?

I have no biology background.

What do you recommend me to read?

Thank you.

I have no deep biology background. What do you recommend me to read? Thank you.

I cannot tell you how to calculate the r^2 values. Sorry, but that is not something I have done without the use of a tool like Paul de Bakker's Tagger program. See de Bakker et al., Nature Genetics Advance Online Publication 23 October 2005 doi:10.1038/ng1669) visit tagger website. Or try Haploview - from HapMap website: For performing in depth LD and Haplotype analysis of genotype data, install Haploview in your local machine. Haploview (ver 4.1) is currently available for download.

Ok! Thank you very much!

I think you can find information you are looking for just here http://www.sph.umich.edu/csg/abecasis/class/666.03.pdf