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AU test (Read 4965 times)
hannah
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AU test
Nov 29th, 2008 at 2:41pm
 
Hi all,

Perhaps I missed it, but is there an implementation of the approximately unbiased test for comparing tree topologies?  It would be great to have the equivalent of CONSEL, showing the p-values from various tests of competing topologies.

Thanks!
Hannah
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Sergei
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Re: AU test
Reply #1 - Dec 1st, 2008 at 7:55am
 
Dear Hannah,

HyPhy only implements the Shimodaira Hasegawa (or its simpler version for 2 trees - Kishino Hasegawa) test. Which AU test are you referring to? Can you provide a reference?

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Sergei
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hannah
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Re: AU test
Reply #2 - Dec 1st, 2008 at 2:01pm
 
The test is described in:

An Approximately Unbiased Test of Phylogenetic Tree Selection
Author(s): Hidetoshi Shimodaira
Source: Systematic Biology, Vol. 51, No. 3 (Jun., 2002), pp. 492-508

I am not at all an expert... but I've seen this test used in publications.  I'd love to hear any thoughts you have on this vs. SH (e.g. for processing GARD results).

Thanks!
hannah

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Sergei
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Re: AU test
Reply #3 - Dec 2nd, 2008 at 8:15am
 
Dear Hannah,

I recall reading this paper years ago (it is very good), but I never got around to implementing the test in HyPhy. Sorry:(

Cheers,
Sergei
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Division of Biomedical Informatics
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University of California San Diego
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