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problem running LocalGARD.bf (Read 8307 times)

rubi YaBB Newbies Offline Feed your monkey! Posts: 9	Re: problem running LocalGARD.bf Reply #15 - Apr 22^nd, 2010 at 7:29am Hi Sergei, I assumed I should only rely on the output of GARDProcessor.bf. Looking at the html output of LocalGARD.bf, indeed I see the "GARD found no evidence of recombination" message. So I guess it means I shouldn't accept such cases? I'm attaching such an example with all the outputs. Thanks again, rubi
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Sergei

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Re: problem running LocalGARD.bf
Reply #16 - Apr 22^nd, 2010 at 2:06pm

Hi Ruby,

LocalGARD is the primary test : is there evidence of recombination (or at least heterotachy) in my data? If not, stop there. If there is, then run GARD_Processor.bf to determine which of the inferred recombination breakpoints can be attributed to phylogenetic incongruence with statistical significance.

Best,
Sergei

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego

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