informative sites/bootstrap

James O. McInerney j.mcinerney at nhm.ac.uk
Tue May 5 10:04:54 EST 1998


Peter,

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.

My 2p-worth.

James

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?
> 
> Peter
-- 
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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,
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