[Mesquitelist] (no subject)

[Peter E. Midford]

I would recommend pruning the tree - otherwise PDAP will treat the removed characters as missing data and, depending on the topology of the tree, might give unexpected results or generate an error.

Peter

On Nov 3, 2010, at 13:17, Victoria Ferrero wrote:

> Hello to everybody, 
> 
> I have been following this list for a while but it is the first time writing...
> 
> I am carrying an independent contrast in PDAP and in the phylogeny I'm using the taxa belonging to two groups of interested which are related along most of the clades. I would like to carry a global analysis (with all taxa) and then an analysis only with the taxa of one group (north distributed) and other with the taxa of the other group (south distributed). In the two latter cases should I prune the original phylogeny to my taxa of interest or should I leave all the taxa and eliminate the characters of the non analysed taxa from the character matrix?
> 
> thanks for the help, 
> 
> Best regards!!
> 
> Victoria
> 
> 
> Victoria Ferrero
> Plant Ecology and Evolution Group
> Centre for Functional Ecology
> Department of Life Sciences,
> Faculty of Science and Technology,
> University of Coimbra
> Apartado 3046
> 3001-401 Coimbra
> Portugal
> 
> 
> 
> 
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--
Peter Midford
Mesquite Developer




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