Puzzling question

James McInerney james.o.mcinerney at may.ie
Fri Feb 25 12:22:39 EST 2000

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.  In
general QP is much more conservative than bootstrapping, certainly in
the deeper branches of the tree.  Is this a general feature of QP or am 
I seeing differences that are due to the method of analysis.  I know it
it difficult to say without performing a direct comparison of the two
methods, but I do not have the computational power at my disposal to
perform 100 bootstraps using the ML or MP criteria.

Here are examples:

81  45  44
100 89  86
92  62  59
100 44  N/A
99  96  80
100 89  91
85  74  N/A
85  31  N/A
77  29  29

There is no instance in the whole majority-rule consensus tree where
either of the QP support values is higher than the NJ-bootstrap support value.

Is it possible that the NJ-bootstrap is being 'too kind'?


             Dr. James O. McInerney,
Dept. Biology,                       Dept. Zoology,
Natl. Univ. Ireland,                 The Natural History Museum,
Maynooth,                  and       Cromwell road,
Co. Kildare, Ireland                 London SW7 5BD, UK.
Phone +353 1 708 3860                +44 171 938 9163
Fax   +353 1 708 3845                +44 171 938 9158
email james.o.mcinerney at may.ie       j.mcinerney at nhm.ac.uk

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