Research Topics
| John P HuelsenbeckSummaryAffiliation: University of Rochester Country: USA Publications
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Detail Information
Publications
A compound poisson process for relaxing the molecular clockJ P Huelsenbeck
Department of Biology, University of Rochester, New York 14627, USA
Genetics 154:1879-92. 2000..This model should prove useful for estimating divergence times when substitution rates vary across lineages...
Empirical and hierarchical Bayesian estimation of ancestral statesJ P Huelsenbeck
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Syst Biol 50:351-66. 2001..We find that the methods are correlated, but that accommodating uncertainty in parameters of the phylogenetic model can make inferences of ancestral states even more uncertain than they would be in an empirical Bayes analysis...- Effect of nonindependent substitution on phylogenetic accuracyJ P Huelsenbeck
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Syst Biol 48:317-28. 1999..Moreover, the rank order of the performance of different methods does not change. However, all phylogenetic methods become less efficient when substitution follows a compound Poisson process... - Testing a covariotide model of DNA substitutionJohn P Huelsenbeck
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Mol Biol Evol 19:698-707. 2002..I show that in nine of the genes examined a covariotide model provides a better explanation of the data than a model that does not allow constraints to change over time... - Geographic origin of human mitochondrial DNA: accommodating phylogenetic uncertainty and model comparisonJohn P Huelsenbeck
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Syst Biol 51:155-65. 2002..The geographic origin of modern human mtDNA is inferred to be in Africa, although support for this hypothesis was ambiguous for data from an early paper... - Inferring the root of a phylogenetic treeJohn P Huelsenbeck
Department of Biology, University of Rochester, Rochester, New York 14627, USA
Syst Biol 51:32-43. 2002..We also examined the performance of the criteria for a tree of four species for which the topology and root position are well supported. Results of the analyses of these data are consistent with the simulation results... - Bayesian inference of phylogeny and its impact on evolutionary biologyJ P Huelsenbeck
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Science 294:2310-4. 2001.... - MRBAYES: Bayesian inference of phylogenetic treesJ P Huelsenbeck
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Bioinformatics 17:754-5. 2001..AVAILABILITY: MRBAYES, including the source code, documentation, sample data files, and an executable, is available at http://brahms.biology.rochester.edu/software.html... - A Bayesian framework for the analysis of cospeciationJ P Huelsenbeck
Department of Biology, University of Rochester, New York 14627, USA
Evolution 54:352-64. 2000..In particular, it does not assume that the host or parasite phylogenies are known without error; many alternative phylogenies are sampled in proportion to their probability of being correct... - Accommodating phylogenetic uncertainty in evolutionary studiesJ P Huelsenbeck
Department of Biology, University of Rochester, Rochester, NY 14627, USA
Science 288:2349-50. 2000..We describe methods for accommodating phylogenetic uncertainty in evolutionary studies by means of Bayesian inference. The methods are computationally intensive but general enough to be applied in most comparative evolutionary studies... - Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inferenceGautam Altekar
Department of Computer Science, University of Rochester, USA
Bioinformatics 20:407-15. 2004..The algorithm has been implemented using two popular parallel programming models: message passing and shared memory. Performance results indicate nearly linear speed improvement in both programming models for small and large data sets...