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testing if seqs. are in same phylo. tree?

Junhyong Kim junkim at peaplant.biology.yale.edu
Wed Nov 15 19:12:26 EST 1995


Hi,

can I get more information on exactly how good the approximation might 
be?

The different tree models differ from each other in the joint 
probability distribution by a linear transformation; therefore, the 
goodness of the approximation should depend on the degree of symmetry 
in the stochastic model. Worse for more symmetric models since the 
alternative models are further away from the null model. Since the chi 
square approximation is based on local Taylor expansion, we've 
speculated that even under the best case, i.e., when the null model is 
in the intersection of different topologies, the chi square 
approximation should be off proportional to the subspace codimension 
difference between what one assumes to be the degrees of freedom for 
the alternative model (I don't know what is normally assumed) and the 
actual (which differs depending on the degree of symmetry of the 
stochastic model)...

Thank you,

Junhyong





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