Puzzling question

Mike Syvanen syvanen at ucdavis.edu
Tue Feb 29 14:52:02 EST 2000

James McInerney wrote:

> Dear all,
> I have a question about the behaviour of Quartet puzzling.  Perhaps
> Korbinian Strimmer is 'listening' so he might be able to shed a bit of light.
> I have a large dataset (119 taxa) and using bootstrapping (NJ) or
> Quartet Puzzling (MP and ML) I get substantially different results.


I would suggest that you break up your data set into smaller groups.
With 119 taxa the number of trees you must consider is about 10^200.
There is no algorthm that can even begin to explore such a large space.  I am not
familiar with quartet puzzling, but have found that when different approaches
give  conflicing results, the best approach is to break up the data set
into smaller ones.

Mike Syvanen


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