Bayesian random local clocks, or one rate to rule them all

[1]  Ming-Hui Chen,et al.  Choosing among Partition Models in Bayesian Phylogenetics , 2010, Molecular biology and evolution.

[2]  Walter Zucchini,et al.  Model Selection , 2011, International Encyclopedia of Statistical Science.

[3]  Peter Beerli,et al.  Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations , 2010, Genetics.

[4]  Simon J. Greenhill,et al.  Language Phylogenies Reveal Expansion Pulses and Pauses in Pacific Settlement , 2009, Science.

[5]  Michael Defoin-Platel,et al.  Clock-constrained tree proposal operators in Bayesian phylogenetic inference , 2008, 2008 8th IEEE International Conference on BioInformatics and BioEngineering.

[6]  Marc A Suchard,et al.  Fully Bayesian tests of neutrality using genealogical summary statistics , 2008, BMC Genetics.

[7]  A. Rambaut,et al.  BEAST: Bayesian evolutionary analysis by sampling trees , 2007, BMC Evolutionary Biology.

[8]  Ziheng Yang.  PAML 4: phylogenetic analysis by maximum likelihood. , 2007, Molecular biology and evolution.

[9]  Ziheng Yang,et al.  Inferring speciation times under an episodic molecular clock. , 2007, Systematic biology.

[10]  Tony O’Hagan.  Bayes factors , 2006 .

[11]  H. Philippe,et al.  Computing Bayes factors using thermodynamic integration. , 2006, Systematic biology.

[12]  S. Ho,et al.  Relaxed Phylogenetics and Dating with Confidence , 2006, PLoS biology.

[13]  M. Suchard,et al.  Models for Estimating Bayes Factors with Applications to Phylogeny and Tests of Monophyly , 2005, Biometrics.

[14]  M. Suchard,et al.  Joint Bayesian estimation of alignment and phylogeny. , 2005, Systematic biology.

[15]  H. Kishino,et al.  Dating of the human-ape splitting by a molecular clock of mitochondrial DNA , 2005, Journal of Molecular Evolution.

[16]  G. Serio,et al.  A new method for calculating evolutionary substitution rates , 2005, Journal of Molecular Evolution.

[17]  Allan C. Wilson,et al.  Mitochondrial DNA sequences of primates: Tempo and mode of evolution , 2005, Journal of Molecular Evolution.

[18]  J. Felsenstein.  Evolutionary trees from DNA sequences: A maximum likelihood approach , 2005, Journal of Molecular Evolution.

[19]  Peter G Foster,et al.  Modeling compositional heterogeneity. , 2004, Systematic biology.

[20]  Ziheng Yang.  Maximum likelihood phylogenetic estimation from DNA sequences with variable rates over sites: Approximate methods , 1994, Journal of Molecular Evolution.

[21]  Kenneth Lange,et al.  Applied Probability , 2003 .

[22]  D. Penny,et al.  The modern molecular clock , 2003, Nature Reviews Genetics.

[23]  M. Suchard,et al.  Testing a molecular clock without an outgroup: derivations of induced priors on branch-length restrictions in a Bayesian framework. , 2003, Systematic biology.

[24]  M. Stanhope,et al.  Local Molecular Clocks in Three Nuclear Genes: Divergence Times for Rodents and Other Mammals and Incompatibility Among Fossil Calibrations , 2003, Journal of Molecular Evolution.

[25]  Alexei J Drummond,et al.  Estimating mutation parameters, population history and genealogy simultaneously from temporally spaced sequence data. , 2002, Genetics.

[26]  M. Sanderson.  Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach. , 2002, Molecular biology and evolution.

[27]  Effrey,et al.  Divergence Time and Evolutionary Rate Estimation with Multilocus Data , 2002 .

[28]  John P. Huelsenbeck,et al.  MRBAYES: Bayesian inference of phylogenetic trees , 2001, Bioinform..

[29]  A. Rodrigo,et al.  The inference of stepwise changes in substitution rates using serial sequence samples. , 2001, Molecular biology and evolution.

[30]  M. Suchard,et al.  Bayesian selection of continuous-time Markov chain evolutionary models. , 2001, Molecular biology and evolution.

[31]  W. Bruno,et al.  Performance of a divergence time estimation method under a probabilistic model of rate evolution. , 2001, Molecular biology and evolution.

[32]  Edward I. George,et al.  The Practical Implementation of Bayesian Model Selection , 2001 .

[33]  Z. Yang,et al.  Estimation of primate speciation dates using local molecular clocks. , 2000, Molecular biology and evolution.

[34]  J. Huelsenbeck,et al.  A compound poisson process for relaxing the molecular clock. , 2000, Genetics.

[35]  B. Larget,et al.  Markov Chain Monte Carlo Algorithms for the Bayesian Analysis of Phylogenetic Trees , 2000 .

[36]  H. Kishino,et al.  Estimating the rate of evolution of the rate of molecular evolution. , 1998, Molecular biology and evolution.

[37]  Michael J. Sanderson,et al.  A Nonparametric Approach to Estimating Divergence Times in the Absence of Rate Constancy , 1997 .

[38]  Ziheng Yang,et al.  PAML: a program package for phylogenetic analysis by maximum likelihood , 1997, Comput. Appl. Biosci..

[39]  Z. Yang,et al.  Among-site rate variation and its impact on phylogenetic analyses. , 1996, Trends in ecology & evolution.

[40]  Jun S. Liu,et al.  The Collapsed Gibbs Sampler in Bayesian Computations with Applications to a Gene Regulation Problem , 1994 .

[41]  E. George,et al.  Journal of the American Statistical Association is currently published by American Statistical Association. , 2007 .

[42]  J. Gillespie.  The causes of molecular evolution , 1991 .

[43]  J H Gillespie,et al.  Lineage effects and the index of dispersion of molecular evolution. , 1989, Molecular biology and evolution.

[44]  T Gojobori,et al.  Molecular phylogeny and evolution of primate mitochondrial DNA. , 1988, Molecular biology and evolution.

[45]  W. K. Hastings,et al.  Monte Carlo Sampling Methods Using Markov Chains and Their Applications , 1970 .

[46]  Vincent M. Sarich,et al.  Immunological Time Scale for Hominid Evolution , 1967, Science.

[47]  L. Pauling,et al.  Evolutionary Divergence and Convergence in Proteins , 1965 .

[48]  N. Metropolis,et al.  Equation of State Calculations by Fast Computing Machines , 1953, Resonance.

[49]  H. Jeffreys.  Some Tests of Significance, Treated by the Theory of Probability , 1935, Mathematical Proceedings of the Cambridge Philosophical Society.

[50]  H. Jeffreys.  The Theory of Probability , 1896 .