As a general reference text to handle phylogentic data and sequences in R, you may have a look at
Paradis (2011) Analysis of Phylogenetics and Evolution in R, 2nd edition. Springer.

Best wishes

Juan A. Balbuena


--

Dr. Juan A. Balbuena
Cavanilles Institute of Biodiversity and Evolutionary Biology
University of Valencia                                           
http://www.uv.es/~balbuena
P.O. Box 22085                                                   
http://www.uv.es/cophylpaco
46071 Valencia, Spain

e-mail:
j.a.balbu...@uv.es    tel. +34 963 543 658    fax +34 963 543 733
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