Hi Ricky

I have not experience with SHAPEIT, but it is rather easy to get a list of haplotype frequencies with package haplo.stats, which works with R statistical package.Shared haplotypes are those with absolute frequencies above 1.

Here you can find a Tutorial on how to use it

http://faculty.washington.edu/kenrice/sisg/haplo.stat.pdf

Hope this helps

Pablo

Hi Ricky,

To analyze haplotypes you can use  DNAsp software (Rozas et al., 2009). See link: http://www.ub.edu/dnasp/

To analyze genotypes depends on your data, if you have microsatellites you can use micro-satellite toolkit, is a package of excel, I can share you the zip file.

I hope this helps

Cheers

Nancy