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Methodology Questions >> How to >> how to do REL/FEL analyses http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1114817177 Message started by dmerl on Apr 29th, 2005 at 4:26pm |
Title: how to do REL/FEL analyses Post by dmerl on Apr 29th, 2005 at 4:26pm
Hi Sergei - last question for today I promise :)
I am trying to use the REL and FEL methods, as described in KPF2005, and I just wanted to make sure that I have chosen the correct settings. I am using the command line version of hyphy. My understanding is that FEL corresponds to: 8 (positive selection) -> 6 (quickly test...) -> 1 (universal code) -> 2 (restore an anlysis...) -> 3 (estimate dn/ds from data with branch corrections) -> 6 (fixed effects, site by site, dS adjusted) -> ... Is this a correct way to do a FEL analysis? Also, is the Random effects likelihood method option 7 under the ancestor counting methods menu? (option 7 is "obtain a site specific distribution of dn and ds") Or are your random effects methods implemented under the "test for positive selection using the method of Nielsen and Yang" menu? once again many thanks, Dan |
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