missing concordance values?

[Genevieve]

Hi!

I've run two BUCKy analyses, 1 with 6 taxa and 1 with 14 taxa. I have 3 splits listed for the primary concordance tree of the 6 taxa set and 11 splits for the primary concordance tree for the 14 taxa set. I don't have concordance factors for the 2 most basal nodes in either tree. Why is that? While I don't care about the concordance factor of the outgroup, I do care about the 2nd deepest node (1st node after the outgroup). 

Thanks!

Geneviève

[Cécile Ané]

Hi Geneviève,
Both the concordance tree and the population tree are unrooted trees, even if you display them with the outgroup to place the root. So with n taxa, there should indeed be n-3 splits with concordance factors. The other splits in the tree are just one single taxon versus all others, when the tree is considered unrooted.
Cecile.

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Cecile Ane
Departments of Statistics and of Botany
University of Wisconsin - Madison
www.stat.wisc.edu/~ane/

CALS statistical consulting lab:
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