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Science 14 December 2001:
Vol. 294. no. 5550, pp. 2310 - 2314
DOI: 10.1126/science.1065889

Review

Bayesian Inference of Phylogeny and Its Impact on Evolutionary Biology

John P. Huelsenbeck,1* Fredrik Ronquist,2 Rasmus Nielsen,3 Jonathan P. Bollback1

As a discipline, phylogenetics is becoming transformed by a flood of molecular data. These data allow broad questions to be asked about the history of life, but also present difficult statistical and computational problems. Bayesian inference of phylogeny brings a new perspective to a number of outstanding issues in evolutionary biology, including the analysis of large phylogenetic trees and complex evolutionary models and the detection of the footprint of natural selection in DNA sequences.

1 Department of Biology, University of Rochester, Rochester, NY 14627, USA.
2 Department of Systematic Zoology, Evolutionary Biology Centre, Uppsala University, Norbyv. 18D, SE-752 36 Uppsala, Sweden.
3 Department of Biometrics, Cornell University, Ithaca, NY 14853-1643, USA.
*   To whom correspondence should be addressed. E-mail: johnh{at}brahms.biology.rochester.edu


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   Abstract »    Full Text »    PDF »
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   Abstract »    Full Text »    PDF »
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