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SBP identifies recombination but GARD doesn't (Read 4572 times)

shris

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Curious HyPhy user

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SBP identifies recombination but GARD doesn't
Jun 5^th, 2014 at 12:04pm

Hi,

I was wondering if someone could help me with the following:
According to the SBP result, the default parameter AIC and cAIC results show that there is recombination in the data (with 100% and 98% support), but when I use GARD, all I see is -nan; GARD found no evidence of recombination

What could have gone wrong? I have attached the result of the SBP

Thanks!
Shris

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: SBP identifies recombination but GARD doesn't Reply #1 - Jun 10^th, 2014 at 9:47am Hi shris, -nan indicates that GARD did not run properly on your alignment. How many sites and how many sequences do you have? Sergei
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shris YaBB Newbies Offline Curious HyPhy user Posts: 2	Re: SBP identifies recombination but GARD doesn't Reply #2 - Jun 17^th, 2014 at 1:35pm Hi Sergei, I rerun the analysis with different parameters and yet get the same information. I have 58 sequences and 539 codons. Not sure what I am not doing correct, or indeed the SBP results don't concur with the GARD output. The job id is 724539233918156. Thanks! Shris
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