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HYPHY Package >> Feature Additions >> AU test
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Message started by hannah on Nov 29th, 2008 at 2:41pm

Title: AU test
Post by hannah on 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

Title: Re: AU test
Post by Sergei on 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?

Cheers,
Sergei

Title: Re: AU test
Post by hannah on 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


Title: Re: AU test
Post by Sergei on 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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