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Covariation on same or different branches? (Read 1781 times)
Catherine Macken
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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?
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Sergei
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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
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Catherine Macken
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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
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Sergei
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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
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