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Can someone explain why I am getting negative d' values using DNAsp? The D, D' and R values are all negative and I have no idea why! Please can someone reply? Thank you x

Hi, I am hoping someone can help me - I want to check if there is LD across a gene locus I am studying. I have accessed the HapMap LD data and managed to download it to give me D', r2 and LOD values between the SNPs within the region of interest. How do you interpret this? I mean - how can I use this info to make judgement on whether there is LD across this region (approximately 200kb region). What do I do with the data? Please help! I have posted on here before and not had a single reply - I would really really appreciate it. Thank you

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!

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