Welcome, Guest. Please Login
YaBB - Yet another Bulletin Board
 
  HomeHelpSearchLogin  
 
Covariation on same or different branches? (Read 3293 times)
Catherine Macken
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 9
Covariation on same or different branches?
Jan 24th, 2013 at 8:28am
 
The thumbnail sketch of the methodology for detecting covariation that is presented on datamonkey.org says that the method finds covariation between sites that change on the same branch of a phylogeny.  However, from my first reading of Poon et al (2007) (PLoS CompBiol: An evolutionary-network model ... ) it was not obvious to me that the method was limited to covariation between sites that changed on the same branch.  Am I missing something in Poon et al?  What is the true story?
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: Covariation on same or different branches?
Reply #1 - Feb 8th, 2013 at 10:02am
 
Hi Catherine,

The power to detect covariation is (loosely) based on the number of branches where two sites have a substitution, i.e. if two sites covaried perfectly, you would see that they always experience concurrent substitutions. In Poon 2007 there was another method about the covariation of RATES, not substitutions -- that is limited to pairs of sites, however, and not implemented in Datamonkey.

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
 
Catherine Macken
YaBB Newbies
*
Offline


Curious HyPhy user

Posts: 9
Re: Covariation on same or different branches?
Reply #2 - Feb 11th, 2013 at 10:04am
 
Hi Sergei:

I think I have answered this question by realizing that unless you have a meaningful of ordering branches, it won't be possible to pick up a signal from covariation such as when a change at one site is permissive for a subsequent change at another site.

The Poon article to which I referred is the one in which you infer a Bayesian network for HIV V-3 , and uses ancestral reconstruction etc.  I don't think we are speaking of the same articles.

Catherine
Back to top
 
 
IP Logged
 
Sergei
YaBB Administrator
*****
Offline


Datamonkeys are forever...

Posts: 1658
UCSD
Gender: male
Re: Covariation on same or different branches?
Reply #3 - Feb 11th, 2013 at 10:16am
 
Hi Catherine,

Right: the paper I was referring to is Multimedia File Viewing and Clickable Links are available for Registered Members only!!  You need to Login Login

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