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Datamonkey MEME outputs a q-value of 1 for all codons (Read 4952 times)
Josť
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Datamonkey MEME outputs a q-value of 1 for all codons
Jan 28th, 2014 at 4:30am
 
Hi,

I have a few alignments that I want to test for episodic selection and I'm trying to use MEME analysis on datamonkey. However, it is always giving me a q-value of 1 for all codons. On the other hand, if I use the hyphy package on my computer with the QuickSelection.bf batch file (there's an option to select MEME), I get a q-value of 0 for all codons. Is any of these values realistic?

Still related with the datamonkey, it asks for no tree file because it generates its own with NeighborJoining. However, nothing is said about any parameters for building the trees. At least nothing similar to what NeighborJoining.bf, from the hyphy package, asks for.

Thanks in advance,
Josť
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Sergei
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Re: Datamonkey MEME outputs a q-value of 1 for all codons
Reply #1 - Jan 28th, 2014 at 9:23am
 
Hi Jose,

"1" is the more realistic number for q-values for a large number of individual level codon tests. Keep in mind however, that we don't recommend using q-values for detecting individual codons under selection, as the test will be too conservative (see Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login and Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login)

I think the q-value calculation in QuickSelectionDetection.bf is buggy.

The Datamonkey NJ tree is built using the TN93 distance model, but you can always include your own with the data you upload to use it instead.

Sergei
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