Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
purifying selection branch-site REL (Read 2035 times)
antdrew
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 1
purifying selection branch-site REL
Jul 30th, 2013 at 12:12pm
 
Hello,

Sorry if this is a silly question but how do I identify purifying selection of branches using branch-site REL? I am looking over the associated publication, Kosakovsky Pond et al., 2011, and I'm assuming that I can extract the information I need from table 2 but I'm not sure.

Best,
Andrew
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: purifying selection branch-site REL
Reply #1 - Aug 7th, 2013 at 1:36pm
 
Hi Andrew,

Branch-site REL does not directly test for purifying selection, so you can't extract the information about it from the results table. You can get an indication of what the selection profile looks like, but there is no formal test. You could readily modify the test to ask questions about dN/dS < 1 (i.e. is there a proportion of sites along a branch where dN/dS), but I think for the vast majority of branches in the vast majority of data sets the answer is yes by default, i.e. one will have to work hard to find branches where no sites evolve with dN/dS < 1.

Can I ask why you wish to run this test?

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