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http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl Theoretical questions >> Sequence Analysis >> Relaxation of constraint http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?num=1267545466 Message started by ofedrigo on Mar 2^nd, 2010 at 7:57am

Title: Relaxation of constraint
Post by ofedrigo on Mar 2^nd, 2010 at 7:57am

Does anyone know a test for testing for lineage specific relaxation of constraint (not positive selection)?
What do you think about using the improved branch-site model (Zhang et al., 2005) and if the alternative model is rejected, looking at the fraction of sites under constraint relaxation estimated by the null model? it seems clumsy to me, but I can't think about another way...

Thanks,

Olivier

Title: Re: Relaxation of constraint
Post by Sergei on Mar 2^nd, 2010 at 3:28pm

Hi Olivier,

I am not a big fan of that particular model (see the attached for the reason why), but I would concur with your assessment that there are no particularly good models to test for this. In fact, what IS relaxation of constraint? Is it merely that the mean dN/dS along a branch is between the [0,1), negatively selected tree average and 1?

Cheers,
Sergei

http://www.hyphy.org/cgi-bin/hyphy_forums/YaBB.pl?action=downloadfile;file=BranchSiteLetter_001.pdf (198 KB | )

Title: Re: Relaxation of constraint
Post by ofedrigo on Mar 2^nd, 2010 at 4:25pm

Sergei,

Thanks for the pdf. This is a very clear and convincing article.

Olivier