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Rooted Vs Unrooted Trees for Branch Site Analysis (Read 2271 times)

Andrew_Roth

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Rooted Vs Unrooted Trees for Branch Site Analysis
Aug 6^th, 2007 at 3:08pm

Hi Sergei,
I am currently working with a data set containing four distinct clades corresponding to gene orthologues. I would like to conduct a branch site analysis and test each of the branches leading into the clades.

I am wondering what effect rooting the tree with one of the clades as an outgroup would have versus using an unrooted tree to conduct the analysis.

Cheers,
Andrew

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Sergei YaBB Administrator Offline Datamonkeys are forever... Posts: 1658 UCSD Gender:	Re: Rooted Vs Unrooted Trees for Branch Site Analy Reply #1 - Aug 8^th, 2007 at 6:28am Dear Andrew, The model used by the branch-site test is time reversible - rooting should have no effect (i.e. the unrooted tree is used in any case). If you see a difference for two rootings of the same tree, this could be an indication of convergence issues. Cheers, Sergei
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Andrew_Roth YaBB Newbies Offline Posts: 17	Re: Rooted Vs Unrooted Trees for Branch Site Analy Reply #2 - Aug 8^th, 2007 at 10:54am Thank you for the help Sergei.
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