TY - JOUR AU - Anderson, F. E. AU - Swofford, D. L. PY - 2004 DA - 2004// TI - Should we be worried about long-branch attraction in real data sets? Investigations using metazoan 18S rDNA JO - Mol Phylogenet Evol VL - 33 UR - https://doi.org/10.1016/j.ympev.2004.06.015 DO - 10.1016/j.ympev.2004.06.015 ID - Anderson2004 ER - TY - JOUR AU - Bollback, J. P. PY - 2002 DA - 2002// TI - Bayesian model adequacy and choice in phylogenetics JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004175 DO - 10.1093/oxfordjournals.molbev.a004175 ID - Bollback2002 ER - TY - JOUR AU - Brown, J. M. PY - 2014 DA - 2014// TI - Detection of Implausible Phylogenetic Inferences Using Posterior Predictive Assessment of Model Fit JO - Syst Biol VL - 63 UR - https://doi.org/10.1093/sysbio/syu002 DO - 10.1093/sysbio/syu002 ID - Brown2014 ER - TY - JOUR AU - Buckley, T. R. AU - Cunningham, C. W. PY - 2002 DA - 2002// TI - The effects of nucleotide substitution model assumptions on estimates of non-parametric bootstrap support JO - Mol Biol Evol VL - 19 UR - https://doi.org/10.1093/oxfordjournals.molbev.a004094 DO - 10.1093/oxfordjournals.molbev.a004094 ID - Buckley2002 ER - TY - JOUR AU - Chernoff, H. AU - Lehmann, E. L. PY - 1954 DA - 1954// TI - The use of Maximum Likelihood Estimates in χ2 Tests for Goodness of Fit JO - Ann Math Stat VL - 25 UR - https://doi.org/10.1214/aoms/1177728726 DO - 10.1214/aoms/1177728726 ID - Chernoff1954 ER - TY - JOUR AU - Choirat, C. AU - Seri, R. PY - 2012 DA - 2012// TI - Estimation in Discrete Parameter Models JO - Stat Sci VL - 27 UR - https://doi.org/10.1214/11-STS371 DO - 10.1214/11-STS371 ID - Choirat2012 ER - TY - JOUR AU - Doyle, V. P. AU - Young, R. E. AU - Naylor, G. J. AU - Brown, J. M. PY - 2015 DA - 2015// TI - Can we identify genes with increased phylogenetic reliability? JO - Syst Biol VL - 64 UR - https://doi.org/10.1093/sysbio/syv041 DO - 10.1093/sysbio/syv041 ID - Doyle2015 ER - TY - JOUR AU - Duchêne, D. A. AU - Duchêne, S. AU - Holmes, E. C. AU - Simon Ho, Y. W. PY - 2015 DA - 2015// TI - Evaluating the Adequacy of Molecular Clock Models Using Posterior Predictive Simulations JO - Mol Biol Evol VL - 32 UR - https://doi.org/10.1093/molbev/msv154 DO - 10.1093/molbev/msv154 ID - Duchêne2015 ER - TY - JOUR AU - Duchêne, S. AU - Di Giallonardo, F. AU - Holmes, E. C. PY - 2016 DA - 2016// TI - Substitution Model Adequacy and Assessing the Reliability of Estimates of Virus Evolutionary Rates and Time Scales JO - Mol Biol Evol VL - 33 UR - https://doi.org/10.1093/molbev/msv207 DO - 10.1093/molbev/msv207 ID - Duchêne2016 ER - TY - STD TI - Duchêne SS, Bouckaert R, Duchêne DA, Stadler T, Drummond AJ. Phylodynamic model adequacy using posterior predictive simulations. bioRxiv. 2018;:255596. ID - ref10 ER - TY - JOUR AU - Dunn, K. A. AU - Kenney, T. AU - Gu, H. AU - Bielawski, J. P. PY - 2019 DA - 2019// TI - Improved inference of site-specific selection pressures under a generalized parametric model of codon evolution JO - BMC Evol Biol VL - 19 UR - https://doi.org/10.1186/s12862-018-1326-7 DO - 10.1186/s12862-018-1326-7 ID - Dunn2019 ER - TY - JOUR AU - Efron, B. PY - 1979 DA - 1979// TI - Bootstrap methods: another look at the jackknife JO - Ann Stat VL - 7 UR - https://doi.org/10.1214/aos/1176344552 DO - 10.1214/aos/1176344552 ID - Efron1979 ER - TY - JOUR AU - Felsenstein, J. PY - 1978 DA - 1978// TI - Cases in which parsimony or compatibility methods will be positively misleading JO - Syst Zool VL - 27 UR - https://doi.org/10.2307/2412923 DO - 10.2307/2412923 ID - Felsenstein1978 ER - TY - JOUR AU - Felsenstein, J. PY - 1985 DA - 1985// TI - Confidence limits on phylogenies: An approach using the bootstrap JO - Evolution VL - 39 UR - https://doi.org/10.1111/j.1558-5646.1985.tb00420.x DO - 10.1111/j.1558-5646.1985.tb00420.x ID - Felsenstein1985 ER - TY - STD TI - Felsenstein J. Inferring Phylogenies.Oxford University Press; 2003. ID - ref15 ER - TY - JOUR AU - Gatesy, J. PY - 2007 DA - 2007// TI - A tenth crucial question regarding model use in phylogenetics JO - Trends Ecol Evol VL - 22 UR - https://doi.org/10.1016/j.tree.2007.08.002 DO - 10.1016/j.tree.2007.08.002 ID - Gatesy2007 ER - TY - JOUR AU - Goldman, N. PY - 1993 DA - 1993// TI - Statistical tests of models of DNA substitution JO - J Mol Evol VL - 36 UR - https://doi.org/10.1007/BF00166252 DO - 10.1007/BF00166252 ID - Goldman1993 ER - TY - JOUR AU - Hammersley, J. M. PY - 1950 DA - 1950// TI - On Estimating Restricted Parameters JO - Journal of the Royal Statistical Society: Series B (Methodological) VL - 12 ID - Hammersley1950 ER - TY - STD TI - Hilton SK, Bloom JD. Modeling site-specific amino-acid preferences deepens phylogenetic estimates of viral sequence divergence. Virus Evol. 2018; 4(2). vey033. ID - ref19 ER - TY - JOUR AU - Huelsenbeck, J. AU - Hillis, D. PY - 1993 DA - 1993// TI - Success of Phylogenetic Methods in the Four-Taxon Case JO - Syst Biol VL - 42 UR - https://doi.org/10.1093/sysbio/42.3.247 DO - 10.1093/sysbio/42.3.247 ID - Huelsenbeck1993 ER - TY - JOUR AU - Huelsenbeck, J. PY - 1995 DA - 1995// TI - Performance of phylogenetic methods in simulation JO - Syst Biol VL - 44 UR - https://doi.org/10.1093/sysbio/44.1.17 DO - 10.1093/sysbio/44.1.17 ID - Huelsenbeck1995 ER - TY - JOUR AU - Kelchner, S. A. AU - Thomas, M. A. PY - 2007 DA - 2007// TI - Model use in phylogenetics: nine key questions JO - Trends Ecol Evol VL - 22 UR - https://doi.org/10.1016/j.tree.2006.10.004 DO - 10.1016/j.tree.2006.10.004 ID - Kelchner2007 ER - TY - JOUR AU - Kenney, T. AU - Gu, H. PY - 2012 DA - 2012// TI - 2012. Hessian Calculation for Phylogenetic Likelihood based on the Pruning Algorithm and its Applications JO - Stat Appl Genet Mol Biol VL - 11 UR - https://doi.org/10.1515/1544-6115.1779 DO - 10.1515/1544-6115.1779 ID - Kenney2012 ER - TY - STD TI - Kenney T, Gu H. 2016. The Adequate Bootstrap (preprint). ArXiv:1608.05913. 2016:57. https://arxiv.org/abs/1608.05913. UR - https://arxiv.org/abs/1608.05913 ID - ref24 ER - TY - STD TI - Moore DS. Chi-square tests In: Hogg RV, editor. Studies in Statistics, Volume 19, The Mathematical Association of America.1978. p. 66–106. ID - ref25 ER - TY - STD TI - Ostrovsky E, Sirota L, Zeldin A. Rate of convergence in the maximum likelihood estimation for partial discrete parameter, with applications to the cluster analysis and philology. 2014. arXiv:1402.6409 [math.ST]. ID - ref26 ER - TY - JOUR AU - Posada, D. AU - Crandall, K. A. PY - 1998 DA - 1998// TI - ModelTest: testing the model of DNA substitution JO - Bioinformatics VL - 14 UR - https://doi.org/10.1093/bioinformatics/14.9.817 DO - 10.1093/bioinformatics/14.9.817 ID - Posada1998 ER - TY - JOUR AU - Posada, D. PY - 2008 DA - 2008// TI - jModelTest: phylogenetic model averaging JO - Mol Biol Evol VL - 25 UR - https://doi.org/10.1093/molbev/msn083 DO - 10.1093/molbev/msn083 ID - Posada2008 ER - TY - JOUR AU - Rao, K. C. AU - Robson, D. S. PY - 1974 DA - 1974// TI - A Chi-squared statistic for goodness-of-fit tests within the exponential family JO - Commun Stat VL - 3 UR - https://doi.org/10.1080/03610927408827216 DO - 10.1080/03610927408827216 ID - Rao1974 ER - TY - JOUR AU - Ripplinger, J. AU - Sullivan, J. PY - 2010 DA - 2010// TI - Assessment of Substitution Model Adequacy Using Frequentist and Bayesian Methods JO - Mol Biol Evol VL - 27 UR - https://doi.org/10.1093/molbev/msq168 DO - 10.1093/molbev/msq168 ID - Ripplinger2010 ER - TY - JOUR AU - Sanderson, M. J. AU - Kim, J. PY - 2000 DA - 2000// TI - Parametric phylogenetics? JO - Syst Biol VL - 49 UR - https://doi.org/10.1080/106351500750049860 DO - 10.1080/106351500750049860 ID - Sanderson2000 ER - TY - JOUR AU - Schenk, J. AU - Hufford, L. PY - 2010 DA - 2010// TI - Effects of Substitution Models on Divergence Time Estimates: Simulations and an Empirical Study of Model Uncertainty Using Cornales JO - Syst Botany VL - 35 UR - https://doi.org/10.1600/036364410792495809 DO - 10.1600/036364410792495809 ID - Schenk2010 ER - TY - JOUR AU - Sullivan, J. AU - Joyce, P. PY - 2005 DA - 2005// TI - Model Selection In Phylogenetics JO - Annu Rev Ecol Evol Syst VL - 36 UR - https://doi.org/10.1146/annurev.ecolsys.36.102003.152633 DO - 10.1146/annurev.ecolsys.36.102003.152633 ID - Sullivan2005 ER - TY - JOUR AU - Sullivan, J. AU - Swofford, D. L. PY - 1997 DA - 1997// TI - Are guinea pigs rodents? The importance of adequate models in molecular phylogenetics JO - J Mamm Evol VL - 4 UR - https://doi.org/10.1023/A:1027314112438 DO - 10.1023/A:1027314112438 ID - Sullivan1997 ER - TY - JOUR AU - Sullivan, J. AU - Swofford, D. L. PY - 2001 DA - 2001// TI - 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? JO - Syst Biol VL - 50 UR - https://doi.org/10.1080/106351501753328848 DO - 10.1080/106351501753328848 ID - Sullivan2001 ER - TY - CHAP AU - Swofford, D. L. AU - Olsen, G. J. AU - Waddell, P. J. AU - Hillis, D. M. ED - Hillis, D. M. ED - Moritz, C. PY - 1996 DA - 1996// TI - Phylogenetic inference BT - Molecular systematics PB - Sinauer Associates CY - Sunderland, Mass ID - Swofford1996 ER - TY - JOUR AU - Swofford, D. L. AU - Waddell, P. J. AU - Huelsenbeck, J. P. AU - Foster, P. G. AU - Lewis, P. O. AU - AND Rogers, J. S. PY - 2001 DA - 2001// TI - Bias in Phylogenetic Estimation and Its Relevance to the Choice between Parsimony and Likelihood Methods JO - Syst Biol VL - 50 UR - https://doi.org/10.1080/10635150117959 DO - 10.1080/10635150117959 ID - Swofford2001 ER - TY - JOUR AU - Waddell, P. J. AU - Ota, R. AU - Penny, D. PY - 2009 DA - 2009// TI - Measuring Fit of Sequence Data to Phylogenetic Model: Gain of Power using Marginal Tests JO - J Mol Evol VL - 69 UR - https://doi.org/10.1007/s00239-009-9268-8 DO - 10.1007/s00239-009-9268-8 ID - Waddell2009 ER - TY - JOUR AU - Yang, Z. AU - Goldman, N. AU - Friday, A. E. PY - 1995 DA - 1995// TI - Maximum likelihood trees from DNA sequences: a peculiar statistical estimation problem JO - Syst Biol VL - 44 UR - https://doi.org/10.1093/sysbio/44.3.384 DO - 10.1093/sysbio/44.3.384 ID - Yang1995 ER - TY - JOUR AU - Yang, Z. AU - Nielsen, R. AU - Goldman, N. AU - Pedersen, A. M. K. PY - 2000 DA - 2000// TI - Codon-substitution models for heterogeneous selection pressure at amino acid sites JO - Genetics VL - 155 ID - Yang2000 ER - TY - JOUR AU - Yang, Z. H. PY - 1994 DA - 1994// TI - Estimating the Pattern of Nucleotide Substitution JO - J Mol Evol VL - 39 ID - Yang1994 ER - TY - JOUR AU - Zharkikh, A. PY - 1994 DA - 1994// TI - Estimation of evolutionary distances between nucleotide sequences JO - J Mol Evol VL - 39 UR - https://doi.org/10.1007/BF00160155 DO - 10.1007/BF00160155 ID - Zharkikh1994 ER -