I believe that you should use all sites during bootstrapping. Each bootstrap
replicate is a pseudo-sample of the universe of sites. It should, therefore,
not be constrained by only sampling the parsimony-informative sites. This
means that in some bootstrap replicates there will be _a lot_ of uninformative
sites, and in some replicates there will be _few_ sites. In the subsequent
analysis of each bootstrapped dataset, the uninformative sites will not
contribute to the phylogeny, however, they should be included in the sampling process.
I'm not a cladist, so maybe somebody more familiar with cladistic analyses
could add to this dscussion.
Peter Schuchert wrote:
>> Please excuse this perhaps naive question. For a
> bootstrap analysis, do you use all sites of an sequence
> alignement or only the informative ones? I checked through
> several papers on molecular phylogenies, but found no details
> in them. Or more general, is it preferrable to work with the
> informative sites only for all analyses?
James O. McInerney email: J.mcinerney at nhm.ac.uk
Molec. Biol. Comput. Officer, phone: +44 171 938 9163
Department of Zoology, Fax: +44 171 938 9158
The Natural History Museum,
London SW7 5BD.