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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Datamonkey Server >> Datamonkey feedback >> FUBAR Outputs http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1351260105 Message started by Dylan Storey on Oct 26^th, 2012 at 7:01am

Title: FUBAR Outputs
Post by Dylan Storey on Oct 26^th, 2012 at 7:01am

FUBAR when run on the server is giving results for sites under positive and negative selection while the HyPhy package only gives positive.

I assume that the negatively selected sites can be parsed simply enough from the CSV but I'd like to know what criteria you guys are using in order to match results as closely as possible.

Thanks in advance for the help!

Title: Re: FUBAR Outputs
Post by Sergei on Oct 26^th, 2012 at 8:52am

Hi Dylan,

Use the appropriate column of the output .csv file (Prob [alpha>beta]) and gate it on whatever posterior probability you are comfortable with.
The default on the server is 0.9.

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Title: Re: FUBAR Outputs
Post by Dylan Storey on Oct 26^th, 2012 at 9:16am

I knew it was simple. Thanks for the quick response!