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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Theoretical questions >> Sequence Analysis >> SBP identifies recombination but GARD doesn't http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1401995042 Message started by shris on Jun 5^th, 2014 at 12:04pm

Title: SBP identifies recombination but GARD doesn't
Post by shris on 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

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=upload_20782653765991_1_SBP_report.txt (32 KB | 1 )

Title: Re: SBP identifies recombination but GARD doesn't
Post by Sergei on 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

Title: Re: SBP identifies recombination but GARD doesn't
Post by shris on 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