I've always thought you could save the shortest trees found after each
bootstrap replicate, then generate a majority rule consensus tree with
these, and that this should be the equivalent of the 'bootstrap tree' (by
bootstrap tree, I mean the one that is output by PAUP at the completion of
a bootstrap analysis). One problem with this is that if some replicates
generate many equally parsimonious trees (say 100), while others only
generate a single (or a few) most parsimonious tree(s), the maj. rule tree
will be overly influenced by those replicates in which many equally
parsimonious trees are found.
I was under the impression that this was also a problem (although
admittedly minor in most cases) with the bootstrap tree, but a friend
tells me that the PAUP bootstrap tree corrects this. Is this the case?
Wollongong, NSW, 2522
Mark_Dowton at uow.edu.au