Package phytools includes a function, findMRCA, that is supposed to work very efficiently with large trees. you may wish to compare it with your function.

Cheers

Juan

--

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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