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Using DEPS in datamonkey (Read 6154 times)
KDO
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Using DEPS in datamonkey
Jun 26th, 2013 at 11:07am
 
Hello,

I wanted to find out whether DEPS in datamonkey is appropriate for finding evidence of directional selection   in domestic pig populations (comprising different breeds) or in livestock in general.  My observation is that DEPS has been used mostly on viruses. Also I tried DEPS on my pig population and got this warning: Protein model selection identified HIV (within host) + F as the best fit model using cAIC, whereas HIV(between hosts) was used for DEPS analysis.  However of all the models listed in DEPS datamonkey there is none called "HIV (within host) + F" that can be chosen for analysis.  Is there some other place in datamonkey where this model can be found?  Thank you.
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Sergei
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Datamonkeys are forever...

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Re: Using DEPS in datamonkey
Reply #1 - Jul 1st, 2013 at 3:22pm
 
Hi KDO,

You should be able to use DEPS (or a faster version of it called FADE) for ANY set of sequences; there is nothing limiting it only to viral sequence analysis.
You can also ignore the warning about the +F part for DEPS analyses -- the frequencies are always estimated by ML, so the warning is not really applicable.

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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KDO
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Re: Using DEPS in datamonkey
Reply #2 - Jul 2nd, 2013 at 9:37am
 
Thanks for the clarification
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