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                                  
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46071 Valencia, Spain

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