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.