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Running DEPS (Read 6485 times)
mo.ber
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Curious HyPhy user

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Running DEPS
Jun 12th, 2013 at 3:33pm
 
Hi, I am a new user of the Datamonkey server. For my analysis I want to determine whether purifying selection is affecting mtDNA in genus of reef fish. From what I've read, it seems that the best approach is to try do determine whether purifying selection is affecting certain branches of a tree, which could be done using DEPS.

I cannot manage to find the DEPS option in the pop-up "Method " menu. Should I be doing this analysis with the aligned mtDNA or translated aminoacid sequence?  Is this option only available in the HYPHY gui?  Undecided

thanks, any information helps
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Sergei
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Datamonkeys are forever...

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Re: Running DEPS
Reply #1 - Jun 13th, 2013 at 2:33pm
 
Hi there,

DEPS (and a newer/faster version called FADE) is available for PROTEIN alignments on Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login.
You should upload your translated alignment and the option will be visible.

Sergei
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