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GARD (Read 3735 times)
Kartik
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GARD
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
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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
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AIC      Yes      46.3      503      100.00%
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Sergei
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Datamonkeys are forever...

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Re: GARD
Reply #1 - Apr 13th, 2011 at 1:44pm
 
Hi kartiks,

GARD uses a more conservative information criterion (small sample AIC, or AIC-c); it requires stronger evidence to declare recombination in an alignment. In your case, SBP should have also found no recombination under AIC-c or BIC. The original manuscript conducted simulations and other comparative studies using AIC-c; AIC is reported by SBP for reference purposes only.

In terms of correcting for the confounding effect recombination, please refer to section 3.10 of Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login for references and discussion.

Sergei
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Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
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Kartik Sunagar
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Re: GARD
Reply #2 - 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  Smiley
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Sergei
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Re: GARD
Reply #3 - 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
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Division of Biomedical Informatics
School of Medicine
University of California San Diego
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Kartik Sunagar
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Re: GARD
Reply #4 - Apr 14th, 2011 at 1:34pm
 
Thank you very much Sir, for the reply Smiley
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