Approximate Likelihood-Ratio Test for Branches: A Fast, Accurate, and Powerful Alternative
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Alfaro, 2003, Bayes or bootstrap? A simulation study comparing the performance of Bayesian Markov chain Monte Carlo sampling and bootstrapping in assessing phylogenetic confidence, Mol. Biol. Evol., 20, 255, 10.1093/molbev/msg028
Berry, 1996, On the interpretation of bootstrap trees: Appropriate threshold of clade selection and induced gain, Mol. Biol. Evol., 13, 999, 10.1093/molbev/13.7.999
Buckley, 2002, Combined data, Bayesian phylogenetics, and the origin of the New Zealand cicada genera, Syst. Biol., 51, 4, 10.1080/106351502753475844
Chernoff, 1954, On the distribution of the likelihood ratio, Ann. Math. Stat., 25, 573, 10.1214/aoms/1177728725
Cowles, 1996, Markov chain Monte Carlo convergence diagnostics: A comparative review, J. Am. Stat. Assoc., 91, 883, 10.1080/01621459.1996.10476956
Cummings, 2003, Comparing bootstrap and posterior probability values in the four-taxon case, Syst. Biol., 52, 477, 10.1080/10635150390218213
Desper, 2004, Theoretical foundationof the balanced minimum evolution method of phylogenetic inference and its relationship to weighted least-squares tree fitting, Mol. Biol. Evol., 21, 587, 10.1093/molbev/msh049
Douady, 2003, Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability, Mol. Biol. Evol., 20, 248, 10.1093/molbev/msg042
Douady, 2003, Molecular phylogenetic evidence refuting the hypothesis of Batoidea (rays and skates) as derived sharks, Mol. Phylogenet. Evol., 25, 215, 10.1016/S1055-7903(02)00333-0
Durbin, 1998, Biological sequence analysis: Probabilistic models of proteins and nucleic acids, 10.1017/CBO9780511790492
Efron, 1996, Bootstrap confidence levels for phylogenetic trees, Proc. Natl. Acad. Sci. USA, 93, 13429, 10.1073/pnas.93.23.13429
Erixon, 2003, Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics, Syst. Biol., 52, 665, 10.1080/10635150390235485
Felsenstein, 1978, Cases in which parsimony or compatibility methods will be positively misleading, Syst. Zool., 27, 401, 10.2307/2412923
Felsenstein, 1985, Confidence intervals on phylogenies: An approach using the bootstrap, Evolution, 39, 783, 10.1111/j.1558-5646.1985.tb00420.x
Felsenstein, 2004, Inferring phylogenies
Felsenstein, 1993, Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull, Syst. Biol., 42, 193, 10.1093/sysbio/42.2.193
Galtier, 2004, Sampling properties of the bootstrap support in molecular phylogeny: Influence of nonindependence among sites, Syst. Biol., 53, 38, 10.1080/10635150490264680
Gaut, 1995, Success of maximum likelihood phylogeny inference in the four-taxon case, Mol. Biol. Evol., 12, 152, 10.1093/oxfordjournals.molbev.a040183
Goldman, 2000, Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics, Mol. Biol. Evol., 17, 975, 10.1093/oxfordjournals.molbev.a026378
Guindon, 2003, A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood, Syst. Biol., 52, 696, 10.1080/10635150390235520
Hillis, 1993, An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis, Syst. Biol., 42, 182, 10.1093/sysbio/42.2.182
Huelsenbeck, 2004, Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models, Syst. Biol., 53, 904, 10.1080/10635150490522629
Huelsenbeck, 2002, Potential applications and pitfalls of Bayesian inference of phylogeny, Syst. Biol., 51, 673, 10.1080/10635150290102366
Huelsenbeck, 2001, MrBayes: Bayesian inference of phylogenetic trees, Bioinformatics, 17, 754, 10.1093/bioinformatics/17.8.754
Huelsenbeck, 2001, Bayesian inference of phylogeny and its impact on evolutionary biology, Science, 294, 2310, 10.1126/science.1065889
Larget, 1999, Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees, Mol. Biol. Evol., 16, 750, 10.1093/oxfordjournals.molbev.a026160
Leaché, 2002, Molecular systematics of the eastern fence lizard (Sceloporus undulatus): A comparison of parsimony, likelihood, and Bayesian approaches, Syst. Biol., 51, 44, 10.1080/106351502753475871
Lewis, 2005, Polytomies and Bayesian phylogenetic inference, Syst. Biol., 54, 241, 10.1080/10635150590924208
Li, 1996, Phylogenetic reconstruction using Markov chain Monte Carlo. Ph.D. dissertation
Mau, 1997, Bayesian phylogenetic inference via Markov chain Monte Carlo methods, Mol. Biol. Evol., 14, 717, 10.1093/oxfordjournals.molbev.a025811
Ota, 2000, Appropriate likelihood ratio tests and marginal distributions for evolutionary tree models with constraints on parameters, Mol. Biol. Evol., 17, 798, 10.1093/oxfordjournals.molbev.a026358
Posada, 1998, ModelTest: Testing the model of DNA substitution, Bioinformatics., 14, 817, 10.1093/bioinformatics/14.9.817
Posada, 2001, Selecting models of nucleotide substitution: An application to human immunodeficiency virus 1 (HIV-1), Mol. Biol. Evol., 18, 897, 10.1093/oxfordjournals.molbev.a003890
Rambaut, 1997, Seq-Gen: An application for the Monte Carlo simulation of DNA sequence evolution along phylogenetic trees, Comput. Appl. Biosci., 13, 235
Rannala, 1996, Probability distribution of molecular evolutionary trees: A new method of phylogenetic inference, J. Mol. Evol., 43, 304, 10.1007/BF02338839
Rokas, 2003, Genome-scale approaches to resolving incongruence in molecular phylogenies, Nature, 425, 798, 10.1038/nature02053
Sanderson, 1995, Objections to bootstrapping phylogenies: A critique, Syst. Biol., 44, 299, 10.1093/sysbio/44.3.299
Self, 1987, Asymptotic properties of maximum likelihood estimators and likelihood ratio tests under nonstandard conditions, J. Am. Stat. Assoc., 82, 605, 10.1080/01621459.1987.10478472
Siddall, 2002, Measures of support, Techniques in molecular systematics and evolution, 80, 10.1007/978-3-0348-8125-8_5
Simmons, 2004, How meaningful are Bayesian support values? Mol, Biol. Evol., 21, 188, 10.1093/molbev/msh014
Stuart, 1999, Kendall's advanced theory of statistics
Sullivan, 2001, Should we use model-based methods for phylogenetic inference when we know that assumptions about among-site rate variation and nucleotide substitution pattern are violated? Syst, Biol., 50, 723
Suzuki, 2002, Overcredibility of molecular phylogenies obtained by Bayesian phylogenetics, Proc. Natl. Acad. Sci. USA, 99, 16138, 10.1073/pnas.212646199
Swofford, 1996, Phylogenetic inference, Molecular systematics, 407
Tateno, 1994, Relative efficiencies of the maximum-likelihood, neighbor-joining, and maximum-parsimony methods when substitution rate varies with site, Mol. Biol. Evol., 11, 261
Taylor, 2004, An assessment of accuracy, error, and conflict with support values from genome-scale phylogenetic data, Mol. Biol. Evol., 21, 1534, 10.1093/molbev/msh156
Waddell, 2002, Very fast algorithms for evaluating the stability of ML and Bayesian phylogenetic trees from sequence data, Genome Inform. Ser. Workshop Genome Inform., 13, 82
Wilcox, 2002, Phylogenetic relationships of the dwarf boas and a comparison of Bayesian and bootstrap measures of phylogenetic support, Mol. Phylogenet. Evol., 25, 361, 10.1016/S1055-7903(02)00244-0
Yang, 1997, PAML: A program package for phylogenetic analysis by maximum likelihood, Comput. Appl. Biosci., 13, 555
Yang, 2000, Codon-substitution models for heterogeneous selection pressure at amino acid sites, Genetics, 155, 431, 10.1093/genetics/155.1.431
Yang, 2005, Branch-length prior influences bayesian posterior probability of phylogeny, Syst. Biol., 54, 455, 10.1080/10635150590945313