Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
Return branches with sites with FUBAR (Read 2046 times)
JorgeT
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 1
Return branches with sites with FUBAR
Oct 17th, 2013 at 8:16am
 
I'm trying to use FUBAR in place of the branch-site REL method in order to enjoy the computational speed-up; however, I do not see a straightforward way to return the branches and sites under selection in the output. I would like to estimate the proportion of sites under positive selection for each branch for 12,000 gene clusters. I'm able to run FUBAR just fine on our cluster non-interactively, it's just a matter of returning for each branch for each site if that site is under selection in the csv output file. Is it feasible for FUBAR to return this lineage-specific information?
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: Return branches with sites with FUBAR
Reply #1 - Oct 31st, 2013 at 3:18pm
 
Hi Jorge,

Unfortunately, there is no way of extracting branch-specific information from FUBAR, as the model explicitly assumes that omega is constant from branch to branch. We have some methods in the works for doing a FUBAR-style branch-site REL model, but those haven't been finished yet

Sergei
Back to top
 

Associate Professor
Division of Infectious Diseases
Division of Biomedical Informatics
School of Medicine
University of California San Diego
WWW WWW  
IP Logged