recombination, LD and haplotypes

[readytogo]

Hi,

 

I have a bunch of genotype data (14 mutations and 312 samples). I have inferred the haplotypes (total of fifteen different haplotypes) and identified that there is LD between three pairs of SNPs. I have done all this using Arlequin and Phase software.

 

What I need to do is identify if any of these haplotypes are the result of recombination. I understand that LD is eroded by recombination but I am just confused by the whole concept. I even get confused with the four gamete test!

 

Can anyone help me with this? I can give more info if needed - i think I have just totally confused myself and I cant find any software that identifies the haplotypes produced by recombination (I have alot more data and will eventually be doing whole gene haplotypes for 60 mutations so I need to get to grips with this now!)

 

Please help!

 

Thanks

 

x

[readytogo]

Does anyone fancy helping me out with this? I just want to know how to identify recombinant haplotypes...or how to do the four gamete test between pairs of mutations when I have 14 mutations.

 

Help!