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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Methodology Questions >> How to >> Best method to study positive selection. http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1385456180 Message started by Kim on Nov 26^th, 2013 at 12:56am

Title: Best method to study positive selection.
Post by Kim on Nov 26^th, 2013 at 12:56am

Hi!

The Datamonkey website recommends MEME for the detection of positive selection. However, I have now heard several times that FUBAR is 'the best' method to detect positive selection at the moment. I know that these methods are not exactly the same, but which one would you recommend to study positive selection?

Thanks!

Title: Re: Best method to study positive selection.
Post by Sergei on Nov 26^th, 2013 at 1:10pm

Hi Kim,

FUBAR can handle much larger datasets, but it only looks for pervasive diversifying selection; MEME can also detect episodic selection (i.e. only a subset of branches) -- hence the methods answer different questions. It doesn't hurt to run both.

Sergei