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Theoretical questions >> Sequence Analysis >> GARD http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1302632617 Message started by Kartik on Apr 12th, 2011 at 11:23am |
Title: GARD Post by Kartik on Apr 12th, 2011 at 11:23am
Hi,
First of all, my apologies if this is a silly question. I'm new to phylogenetics. When I run GARD and SPB analyses on datamonkey server, GARD tells me that it did not find any evidence for recombination. SPB on the other hand identifies '503' as a possible position for recombination. I want to know... 1. Am I interpreting the results wrongly? Are the two algorithms used for different purposes? 2. If SPB is correct and if there is a breakpoint at the particular position, then will it have an impact on the selection analyses (site models and branch-site models)? 3. If it does have an impact, then can I overcome this problem by dividing the alignment into two partitions (1-503 and the rest) and carryout the selection analyses? Thank you very much, Kartik PS: Datamonkey and hyphy rock! GARD --------- The alignment contained 430 potential breakpoints, translating into the search space of 430 models with up to 1 breakpoints of which 350.93% was explored by the genetic algorithm. Recombination report GARD found no evidence of recombination SPB ------ AIC Yes 46.3 503 100.00% |
Title: Re: GARD Post by Kartik Sunagar on Apr 13th, 2011 at 2:14pm
Dear Sir,
Thank you very much for the reply. When you say SBP results under AIC should be used just for reference, does it mean I should consider the results of GARD? That there is no recombination in the dataset? Thank you very much for your time, Yours Sincerely, Kartik :) |
Title: Re: GARD Post by Sergei on Apr 13th, 2011 at 4:29pm
Hi Kartik,
Yes, please use the results of GARD and SBP under AIC-c. From what I recall from my simulations in 2005, AIC gives a lot of false positives, and BIC -- too many false negatives, hence they are not recommended as the default criterion. Sergei |
Title: Re: GARD Post by Kartik Sunagar on Apr 14th, 2011 at 1:34pm
Thank you very much Sir, for the reply :)
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