if you can generate a multiple alignment of DNA sequences (or markers) I
guess you can, if this is for very closely related sequences though you
might want to use an ascertainment bias correction, I'd need a bit more
info about the data though to be able to give a more informed answer,
alexis
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Alexandros (Alexis) Stamatakis
Research Group Leader, Heidelberg Institute for Theoretical Studies
Full Professor, Dept. of Informatics, Karlsruhe Institute of Technology
Adjunct Professor, Dept. of Ecology and Evolutionary Biology, University
of Arizona at Tucson
www.exelixis-lab.org