HyPhy message board - Print Page

HyPhy message board
http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Datamonkey Server >> Datamonkey feedback >> FUBAR on Datamonkey http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1381359166 Message started by ursulla82 on Oct 9^th, 2013 at 3:52pm

Title: FUBAR on Datamonkey
Post by ursulla82 on Oct 9^th, 2013 at 3:52pm

Dear Sergei,

I am using FUBAR through the Datamonkey website and I wonder what the omega in the result page refers to. Is it the beta/alpha ratio? It is greater than one but my genes are globally under negative selection with not a single site under positive selection.

Also, is it possible to get the global dN/dS using FUBAR?

Many thanks,
Ursulla

Title: Re: FUBAR on Datamonkey
Post by Sergei on Oct 9^th, 2013 at 4:05pm

Hi Ursulla,

Because we allow dS and dN to vary in FUBAR (and dS can become very small), the omega ratio will generally be quite unstable. It is better to look at the beta-alpha (which is like dN-dS) and compare it to 0.

Sergei