Puzzling question

[James McInerney]

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:

NJ  ML  MP
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'?


James


-- 
             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
http://www.may.ie/academic/biology/jmbioinformatics.shtml
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