Actually, you can use the web tools sheSis and haploview4.2 separately. LD analysis works well with Haploview 4.2 as well. But the SheSis tool (http://analysis.bio-x.cn) is what I've found to be the best for just haplotype analysis. There, you may use a tool in the simplest way possible, and there you will also find a promt helping corner. It's the simplest route, to put it simply. Many thanks.