International Journal of Plant Genomics
Volume 2008 (2008), Article ID 683509, 16 pages
doi:10.1155/2008/683509
Review Article

Phylogenetic Analyses: A Toolbox Expanding towards Bayesian Methods

Stéphane Aris-Brosou1,2 and Xuhua Xia1

1Department of Biology, Centre for Advanced Research in Environmental Genomics, University of Ottawa, Ontario K1N 6N5, Canada
2Department of Mathematics and Statistics, University of Ottawa, Ontario K1N 6N5, Canada

Received 30 November 2007; Accepted 12 February 2008

Academic Editor: Chunguang Du

Copyright © 2008 Stéphane Aris-Brosou and Xuhua Xia. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. C. Darwin, On the Origin of Species by Means of Natural Selection, J. Murray, London, UK, 1859.
  2. R. R. Sokal and P. H. A. Sneath, Principles of Numerical Taxonomy, W. H. Freeman, San Francisco, Calif, USA, 1963.
  3. L. L. Cavalli-Sforza, I. Barrai, and A. W. Edwards, “Analysis of human evolution under random genetic drift,” Cold Spring Harbor Symposia on Quantitative Biology, vol. 29, 9 pages, 1964.
  4. J. Felsenstein, Inferring Phylogenies, Sinauer Associates, Sunderland, Mass, USA, 2004.
  5. H. Glenner, A. J. Hansen, M. V. Sørensen, F. Ronquist, J. P. Huelsenbeck, and E. Willerslev, “Bayesian inference of the metazoan phylogeny: a combined molecular and morphological approach,” Current Biology, vol. 14, no. 18, 1644 pages, 2004.
  6. B. E. Pfeil, J. A. Schlueter, R. C. Shoemaker, and J. J. Doyle, “Placing paleopolyploidy in relation to taxon divergence: a phylogenetic analysis in legumes using 39 gene families,” Systematic Biology, vol. 54, no. 3, 441 pages, 2005.
  7. E. R. Chare and E. C. Holmes, “A phylogenetic survey of recombination frequency in plant RNA viruses,” Archives of Virology, vol. 151, no. 5, 933 pages, 2006.
  8. H. Philippe and C. J. Douady, “Horizontal gene transfer and phylogenetics,” Current Opinion in Microbiology, vol. 6, no. 5, 498 pages, 2003.
  9. R. Nielsen, C. Bustamante, A. G. Clark, et al., “A scan for positively selected genes in the genomes of humans and chimpanzees,” PLoS Biology, vol. 3, no. 6, e170 pages, 2005.
  10. S. R. Ramírez, B. Gravendeel, R. B. Singer, C. R. Marshall, and N. E. Pierce, “Dating the origin of the Orchidaceae from a fossil orchid with its pollinator,” Nature, vol. 448, no. 7157, 1042 pages, 2007.
  11. R. D. Knight, S. J. Freeland, and L. F. Landweber, “Rewiring the keyboard: evolvability of the genetic code,” Nature Reviews Genetics, vol. 2, no. 1, 49 pages, 2001.
  12. J. Antonovics, M. E. Hood, and C. H. Baker, “Molecular virology: was the 1918 flu avian in origin?,” Nature, vol. 440, no. 7088, E9 pages, 2006, discussion E9-10.
  13. A. P. Jackson and M. A. Charleston, “A cophylogenetic perspective of RNA-virus evolution,” Molecular Biology and Evolution, vol. 21, no. 1, 45 pages, 2004.
  14. J. P. Huelsenbeck, B. Rannala, and B. Larget, “A Bayesian framework for the analysis of cospeciation,” Evolution, vol. 54, no. 2, 352 pages, 2000.
  15. M. Hajibabaei, G. A. C. Singer, P. D. N. Hebert, and D. A. Hickey, “DNA barcoding: how it complements taxonomy, molecular phylogenetics and population genetics,” Trends in Genetics, vol. 23, no. 4, 167 pages, 2007.
  16. S.-J. Luo, J.-H. Kim, W. E. Johnson, et al., “Phylogeography and genetic ancestry of tigers (Panthera tigris),” PLoS Biology, vol. 2, no. 12, e442 pages, 2004.
  17. C. J. Howe, A. C. Barbrook, M. Spencer, P. Robinson, B. Bordalejo, and L. R. Mooney, “Manuscript evolution,” Endeavour, vol. 25, no. 3, 121 pages, 2001.
  18. R. D. Gray and Q. D. Atkinson, “Language-tree divergence times support the Anatolian theory of Indo-European origin,” Nature, vol. 426, no. 6965, 435 pages, 2003.
  19. D. M. Hillis and J. P. Huelsenbeck, “Support for dental HIV transmission,” Nature, vol. 369, no. 6475, 24 pages, 1994.
  20. A. Salas, H.-J. Bandelt, V. Macaulay, and M. B. Richards, “Phylogeographic investigations: the role of trees in forensic genetics,” Forensic Science International, vol. 168, no. 1, 1 pages, 2007.
  21. D. Sankoff and J. H. Nadeau, “Chromosome rearrangements in evolution: from gene order to genome sequence and back,” Proceedings of the National Academy of Sciences of the United States of America, vol. 100, no. 20, 11188 pages, 2003.
  22. D. L. Swofford, P. J. Waddell, J. P. Huelsenbeck, P. G. Foster, P. O. Lewis, and J. S. Rogers, “Bias in phylogenetic estimation and its relevance to the choice between parsimony and likelihood methods,” Systematic Biology, vol. 50, no. 4, 525 pages, 2001.
  23. M. Holder and P. O. Lewis, “Phylogeny estimation: traditional and Bayesian approaches,” Nature Reviews Genetics, vol. 4, no. 4, 275 pages, 2003.
  24. A. Siepel and D. Haussler, “Phylogenetic hidden Markov models,” in Statistical Methods in Molecular Evolution, R. Nielsen, Ed., p. 325, Springer, New York, NY, USA, 2005.
  25. M. Pagel and A. Meade, “Bayesian analysis of correlated evolution of discrete characters by reversible-jump Markov chain Monte Carlo,” American Naturalist, vol. 167, no. 6, 808 pages, 2006.
  26. S. Kumar and A. Filipski, “Multiple sequence alignment: in pursuit of homologous DNA positions,” Genome Research, vol. 17, no. 2, 127 pages, 2007.
  27. C. Notredame, “Recent evolutions of multiple sequence alignment algorithms,” PLoS Computational Biology, vol. 3, no. 8, e123 pages, 2007.
  28. R. C. Edgar and S. Batzoglou, “Multiple sequence alignment,” Current Opinion in Structural Biology, vol. 16, no. 3, 368 pages, 2006.
  29. X. Xia and Z. Xie, “DAMBE: software package for data analysis in molecular biology and evolution,” Journal of Heredity, vol. 92, no. 4, 371 pages, 2001.
  30. S. Kumar, K. Tamura, and M. Nei, “MEGA: molecular evolutionary genetics analysis software for microcomputers,” Computer Applications in the Biosciences, vol. 10, no. 2, 189 pages, 1994.
  31. K. Tamura, J. Dudley, M. Nei, and S. Kumar, “MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4.0,” Molecular Biology and Evolution, vol. 24, no. 8, 1596 pages, 2007.
  32. C. B. Do, M. S. P. Mahabhashyam, M. Brudno, and S. Batzoglou, “ProbCons: probabilistic consistency-based multiple sequence alignment,” Genome Research, vol. 15, no. 2, 330 pages, 2005.
  33. I. M. Wallace, G. Blackshields, and D. G. Higgins, “Multiple sequence alignments,” Current Opinion in Structural Biology, vol. 15, no. 3, 261 pages, 2005.
  34. I. M. Wallace, O. O'Sullivan, D. G. Higgins, and C. Notredame, “M-Coffee: combining multiple sequence alignment methods with T-Coffee,” Nucleic Acids Research, vol. 34, no. 6, 1692 pages, 2006.
  35. B. G. Hall, Phylogenetic Trees Made Easy: A How-to Manual, Sinauer Associates, Sunderland, Mass, USA, 2008.
  36. B. Larget and D. L. Simon, “Markov chain Monte Carlo algorithms for the Bayesian analysis of phylogenetic trees,” Molecular Biology and Evolution, vol. 16, no. 6, 750 pages, 1999.
  37. M. Pagel and A. Meade, “A phylogenetic mixture model for detecting pattern-heterogeneity in gene sequence or character-state data,” Systematic Biology, vol. 53, no. 4, 571 pages, 2004.
  38. B. D. Redelings and M. A. Suchard, “Joint Bayesian estimation of alignment and phylogeny,” Systematic Biology, vol. 54, no. 3, 401 pages, 2005.
  39. A. J. Drummond and A. Rambaut, “BEAST: Bayesian evolutionary analysis by sampling trees,” BMC Evolutionary Biology, vol. 7, article 214, 1 pages, 2007.
  40. H. Shimodaira and M. Hasegawa, “CONSEL: for assessing the confidence of phylogenetic tree selection,” Bioinformatics, vol. 17, no. 12, 1246 pages, 2001.
  41. D. Zwickl, Genetic algorithm approaches for the phylogenetic analysis of large biological sequence datasets under the maximum likelihood criterion, Ph.D. thesis, University of Texas at Austin, Austin, Tex, USA, 2006.
  42. S. L. Kosakovsky Pond, S. D. W. Frost, and S. V. Muse, “HyPhy: hypothesis testing using phylogenies,” Bioinformatics, vol. 21, no. 5, 676 pages, 2005.
  43. F. Ronquist and J. P. Huelsenbeck, “MrBayes 3: Bayesian phylogenetic inference under mixed models,” Bioinformatics, vol. 19, no. 12, 1572 pages, 2003.
  44. G. Altekar, S. Dwarkadas, J. P. Huelsenbeck, and F. Ronquist, “Parallel Metropolis coupled Markov chain Monte Carlo for Bayesian phylogenetic inference,” Bioinformatics, vol. 20, no. 3, 407 pages, 2004.
  45. J. L. Thorne, H. Kishino, and I. S. Painter, “Estimating the rate of evolution of the rate of molecular evolution,” Molecular Biology and Evolution, vol. 15, no. 12, 1647 pages, 1998.
  46. H. Kishino, J. L. Thorne, and W. J. Bruno, “Performance of a divergence time estimation method under a probabilistic model of rate evolution,” Molecular Biology and Evolution, vol. 18, no. 3, 352 pages, 2001.
  47. J. L. Thorne and H. Kishino, “Divergence time and evolutionary rate estimation with multilocus data,” Systematic Biology, vol. 51, no. 5, 689 pages, 2002.
  48. D. J. Wilson and G. McVean, “Estimating diversifying selection and functional constraint in the presence of recombination,” Genetics, vol. 172, no. 3, 1411 pages, 2006.
  49. Z. Yang, “PAML: a program package for phylogenetic analysis by maximum likelihood,” Computer Applications in the Biosciences, vol. 13, no. 5, 555 pages, 1997.
  50. Z. Yang, “PAML 4: phylogenetic analysis by maximum likelihood,” Molecular Biology and Evolution, vol. 24, no. 8, 1586 pages, 2007.
  51. D. L. Swofford, “PAUP: Phylogenetic Analysis Using Parsimony (and other Methods) 4.0 Beta,” Sinauer Associates, Sunderland, Mass, USA, 10th edition, 2002.
  52. N. Lartillot and H. Philippe, “Computing Bayes factors using thermodynamic integration,” Systematic Biology, vol. 55, no. 2, 195 pages, 2006.
  53. S. Guindon and O. Gascuel, “A simple, fast, and accurate algorithm to estimate large phylogenies by maximum likelihood,” Systematic Biology, vol. 52, no. 5, 696 pages, 2003.
  54. A. Stamatakis, “RAxML-VI-HPC: maximum likelihood-based phylogenetic analyses with thousands of taxa and mixed models,” Bioinformatics, vol. 22, no. 21, 2688 pages, 2006.
  55. M. J. Sanderson, “r8s: inferring absolute rates of molecular evolution and divergence times in the absence of a molecular clock,” Bioinformatics, vol. 19, no. 2, 301 pages, 2003.
  56. K. M. Kjer, “Use of rRNA secondary structure in phylogenetic studies to identify homologous positions: an example of alignment and data presentation from the frogs,” Molecular Phylogenetics and Evolution, vol. 4, no. 3, 314 pages, 1995.
  57. C. Notredame, E. A. O'Brien, and D. G. Higgins, “RAGA: RNA sequence alignment by genetic algorithm,” Nucleic Acids Research, vol. 25, no. 22, 4570 pages, 1997.
  58. R. E. Hickson, C. Simon, and S. W. Perrey, “The performance of several multiple-sequence alignment programs in relation to secondary-structure features for an rRNA sequence,” Molecular Biology and Evolution, vol. 17, no. 4, 530 pages, 2000.
  59. X. Xia, “Phylogenetic relationship among horseshoe crab species: effect of substitution models on phylogenetic analyses,” Systematic Biology, vol. 49, no. 1, 87 pages, 2000.
  60. X. Xia, Z. Xie, and K. M. Kjer, “18S ribosomal RNA and tetrapod phylogeny,” Systematic Biology, vol. 52, no. 3, 283 pages, 2003.
  61. J. D. Thompson, D. G. Higgins, and T. J. Gibson, “CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice,” Nucleic Acids Research, vol. 22, no. 22, 4673 pages, 1994.
  62. M. A. Larkin, G. Blackshields, N. P. Brown, et al., “Clustal W and clustal X version 2.0,” Bioinformatics, vol. 23, no. 21, 2947 pages, 2007.
  63. T. Golubchik, M. J. Wise, S. Easteal, and L. S. Jermiin, “Mind the gaps: evidence of bias in estimates of multiple sequence alignments,” Molecular Biology and Evolution, vol. 24, no. 11, 2433 pages, 2007.
  64. G. Landan and D. Graur, “Heads or tails: a simple reliability check for multiple sequence alignments,” Molecular Biology and Evolution, vol. 24, no. 6, 1380 pages, 2007.
  65. A. S. Schwartz, E. W. Myers, and L. Pachter, “Alignment metric accuracy,” http://arxiv.org/abs/q-bio.QM/0510052, 2005.
  66. J. Zhu, J. S. Liu, and C. E. Lawrence, “Bayesian adaptive sequence alignment algorithms,” Bioinformatics, vol. 14, no. 1, 25 pages, 1998.
  67. I. Holmes and W. J. Bruno, “Evolutionary HMMs: a Bayesian approach to multiple alignment,” Bioinformatics, vol. 17, no. 9, 803 pages, 2001.
  68. J. L. Jensen and J. Hein, “Gibbs sampler for statistical multiple alignment,” Statistica Sinica, vol. 15, no. 4, 889 pages, 2005.
  69. M. Clamp, J. Cuff, S. M. Searle, and G. J. Barton, “The Jalview Java alignment editor,” Bioinformatics, vol. 20, no. 3, 426 pages, 2004.
  70. D. Sankoff and R. Cedergren, “Simultaneous comparison of three or more sequences related by a tree,” in Time Wraps, String Edits and Macromolecules: The Theory and Practice of Sequence Comparison, D. Sankoff and R. Cedergren, Eds., p. 253, Addison-Wesley, Reading, Mass, USA, 1983.
  71. J. Hein, “A new method that simultaneously aligns and reconstructs ancestral sequences for any number of homologous sequences, when the phylogeny is given,” Molecular Biology and Evolution, vol. 6, no. 6, 649 pages, 1989.
  72. G. Lunter, I. Miklós, A. Drummond, J. L. Jensen, and J. Hein, “Bayesian coestimation of phylogeny and sequence alignment,” BMC Bioinformatics, vol. 6, article 83, 1 pages, 2005.
  73. K. M. Wong, M. A. Suchard, and J. P. Huelsenbeck, “Alignment uncertainty and genomic analysis,” Science, vol. 319, no. 5862, 473 pages, 2008.
  74. G. Lunter, A. Rocco, N. Mimouni, A. Heger, A. Caldeira, and J. Hein, “Uncertainty in homology inferences: assessing and improving genomic sequence alignment,” Genome Research, vol. 18, no. 2, 298 pages, 2008.
  75. M. Nei and S. Kumar, Molecular Evolution and Phylogenetics, Oxford University Press, New York, NY, USA, 2000.
  76. T. H. Jukes and C. R. Cantor, “Evolution of protein molecules,” in Mammalian Protein Metabolism, H. N. Munro, Ed., p. 21, Academic Press, New York, NY, USA, 1969.
  77. M. Kimura, “A simple method for estimating evolutionary rates of base substitutions through comparative studies of nucleotide sequences,” Journal of Molecular Evolution, vol. 16, no. 2, 111 pages, 1980.
  78. M. Hasegawa, H. Kishino, and T. Yano, “Dating of the human-ape splitting by a molecular clock of mitochondrial DNA,” Journal of Molecular Evolution, vol. 22, no. 2, 160 pages, 1985.
  79. K. Tamura and M. Nei, “Estimation of the number of nucleotide substitutions in the control region of mitochondrial DNA in humans and chimpanzees,” Molecular Biology and Evolution, vol. 10, no. 3, 512 pages, 1993.
  80. S. Tavare, “Some probabilistic and statistical problems on the analysis of DNA sequences,” in Lectures on Mathematics in the Life Sciences, vol. 17, p. 57, American Mathematical Society, Providence, RI, USA, 1986.
  81. Z. Yang, “Maximum-likelihood estimation of phylogeny from DNA sequences when substitution rates differ over sites,” Molecular Biology and Evolution, vol. 10, no. 6, 1396 pages, 1993.
  82. Z. Yang, “Estimating the pattern of nucleotide substitution,” Journal of Molecular Evolution, vol. 39, no. 1, 105 pages, 1994.
  83. N. Goldman and S. Whelan, “A novel use of equilibrium frequencies in models of sequence evolution,” Molecular Biology and Evolution, vol. 19, no. 11, 1821 pages, 2002.
  84. P. Liò and N. Goldman, “Models of molecular evolution and phylogeny,” Genome Research, vol. 8, no. 12, 1233 pages, 1998.
  85. S. Whelan, P. Liò, and N. Goldman, “Molecular phylogenetics: state-of-the-art methods for looking into the past,” Trends in Genetics, vol. 17, no. 5, 262 pages, 2001.
  86. K. P. Burnham and D. R. Anderson, Model Selection and Multimodel Inference : A Practical Information-Theoretic Approach, Springer, New York, NY, USA, 2002.
  87. W. J. Bruno and A. L. Halpern, “Topological bias and inconsistency of maximum likelihood using wrong models,” Molecular Biology and Evolution, vol. 16, no. 4, 564 pages, 1999.
  88. D. Posada and K. A. Crandall, “Selecting the best-fit model of nucleotide substitution,” Systematic Biology, vol. 50, no. 4, 580 pages, 2001.
  89. D. R. Cox, “Further results on tests of separate families of hypotheses,” Journal of the Royal Statistical Society. Series B, vol. 24, no. 2, 406 pages, 1962.
  90. N. Goldman and S. Whelan, “Statistical tests of gamma-distributed rate heterogeneity in models of sequence evolution in phylogenetics,” Molecular Biology and Evolution, vol. 17, no. 6, 975 pages, 2000.
  91. M. Anisimova and O. Gascuel, “Approximate likelihood-ratio test for branches: a fast, accurate, and powerful alternative,” Systematic Biology, vol. 55, no. 4, 539 pages, 2006.
  92. D. Posada and K. A. Crandall, “MODELTEST: testing the model of DNA substitution,” Bioinformatics, vol. 14, no. 9, 817 pages, 1998.
  93. E. Paradis, J. Claude, and K. Strimmer, “APE: analyses of phylogenetics and evolution in R language,” Bioinformatics, vol. 20, no. 2, 289 pages, 2004.
  94. D. Posada, “ModelTest server: a web-based tool for the statistical selection of models of nucleotide substitution online,” Nucleic Acids Research, vol. 34, web server issue, W700 pages, 2006.
  95. F. Abascal, R. Zardoya, and D. Posada, “ProtTest: selection of best-fit models of protein evolution,” Bioinformatics, vol. 21, no. 9, 2104 pages, 2005.
  96. D. Posada and T. R. Buckley, “Model selection and model averaging in phylogenetics: advantages of akaike information criterion and Bayesian approaches over likelihood ratio tests,” Systematic Biology, vol. 53, no. 5, 793 pages, 2004.
  97. D. Pol, “Empirical problems of the hierarchical likelihood ratio test for model selection,” Systematic Biology, vol. 53, no. 6, 949 pages, 2004.
  98. C. M. Hurvich and C.-L. Tsai, “Regression and time series model selection in small samples,” Biometrika, vol. 76, no. 2, 297 pages, 1989.
  99. G. Schwarz, “Estimating the dimension of a model,” Annals of Statistics, vol. 6, no. 2, 461 pages, 1978.
  100. V. N. Minin, Z. Abdo, P. Joyce, and J. Sullivan, “Performance-based selection of likelihood models for phylogeny estimation,” Systematic Biology, vol. 52, no. 5, 674 pages, 2003.
  101. Z. Abdo, V. N. Minin, P. Joyce, and J. Sullivan, “Accounting for uncertainty in the tree topology has little effect on the decision-theoretic approach to model selection in phylogeny estimation,” Molecular Biology and Evolution, vol. 22, no. 3, 691 pages, 2005.
  102. L. Bao, H. Gu, K. A. Dunn, and J. P. Bielawski, “Methods for selecting fixed-effect models for heterogeneous codon evolution, with comments on their application to gene and genome data,” BMC Evolutionary Biology, vol. 7, supplement 1, S5 pages, 2007.
  103. M. A. Suchard, R. E. Weiss, and J. S. Sinsheimer, “Bayesian selection of continuous-time Markov chain evolutionary models,” Molecular Biology and Evolution, vol. 18, no. 6, 1001 pages, 2001.
  104. J. P. Huelsenbeck, B. Larget, and M. E. Alfaro, “Bayesian phylogenetic model selection using reversible jump Markov chain Monte Carlo,” Molecular Biology and Evolution, vol. 21, no. 6, 1123 pages, 2004.
  105. N. Saitou and M. Nei, “The neighbor-joining method: a new method for reconstructing phylogenetic trees,” Molecular Biology and Evolution, vol. 4, no. 4, 406 pages, 1987.
  106. O. Gascuel and M. Steel, “Neighbor-joining revealed,” Molecular Biology and Evolution, vol. 23, no. 11, 1997 pages, 2006.
  107. W. J. Bruno, N. D. Socci, and A. L. Halpern, “Weighted neighbor-joining: a likelihood-based approach to distance-based phylogeny reconstruction,” Molecular Biology and Evolution, vol. 17, no. 1, 189 pages, 2000.
  108. S. L. Baldauf, “Phylogeny for the faint of heart: a tutorial,” Trends in Genetics, vol. 19, no. 6, 345 pages, 2003.
  109. L. L. Cavalli-Sforza and A. W. F. Edwards, “Phylogenetic analysis. Models and estimation procedures,” American Journal of Human Genetics, vol. 19, no. 3, part 1, 233 pages, 1967.
  110. S. Whelan, “New approaches to phylogenetic tree search and their application to large numbers of protein alignments,” Systematic Biology, vol. 56, no. 5, 727 pages, 2007.
  111. M. T. Holder, P. O. Lewis, D. L. Swofford, and B. Larget, “Hastings ratio of the LOCAL proposal used in Bayesian phylogenetics,” Systematic Biology, vol. 54, no. 6, 961 pages, 2005.
  112. J. Felsenstein, “Confidence limits on phylogenies: an approach using the bootstrap,” Evolution, vol. 39, no. 4, 783 pages, 1985.
  113. D. M. Hillis and J. J. Bull, “An empirical test of bootstrapping as a method for assessing confidence in phylogenetic analysis,” Systematic Biology, vol. 42, no. 2, 182 pages, 1993.
  114. J. Felsenstein and H. Kishino, “Is there something wrong with the bootstrap on phylogenies? A reply to Hillis and Bull,” Systematic Biology, vol. 42, no. 2, 193 pages, 1993.
  115. Z. Yang and B. Rannala, “Branch-length prior influences Bayesian posterior probability of phylogeny,” Systematic Biology, vol. 54, no. 3, 455 pages, 2005.
  116. V. Berry and O. Gascuel, “On the interpretation of bootstrap trees: appropriate threshold of clade selection and induced gain,” Molecular Biology and Evolution, vol. 13, no. 7, 999 pages, 1996.
  117. B. Efron, E. Halloran, and S. Holmes, “Bootstrap confidence levels for phylogenetic trees,” Proceedings of the National Academy of Sciences of the United States of America, vol. 93, no. 14, 7085 pages, 1996.
  118. B. Mau, M. A. Newton, and B. Larget, “Bayesian phylogenetic inference via Markov chain Monte Carlo methods,” Biometrics, vol. 55, no. 1, 1 pages, 1999.
  119. J. P. Huelsenbeck, F. Ronquist, R. Nielsen, and J. P. Bollback, “Bayesian inference of phylogeny and its impact on evolutionary biology,” Science, vol. 294, no. 5550, 2310 pages, 2001.
  120. W. J. Murphy, E. Eizirik, S. J. O'Brien, et al., “Resolution of the early placental mammal radiation using Bayesian phylogenetics,” Science, vol. 294, no. 5550, 2348 pages, 2001.
  121. C. J. Douady, F. Delsuc, Y. Boucher, W. F. Doolittle, and E. J. P. Douzery, “Comparison of Bayesian and maximum likelihood bootstrap measures of phylogenetic reliability,” Molecular Biology and Evolution, vol. 20, no. 2, 248 pages, 2003.
  122. M. P. Cummings, S. A. Handley, D. S. Myers, D. L. Reed, A. Rokas, and K. Winka, “Comparing bootstrap and posterior probability values in the four-taxon case,” Systematic Biology, vol. 52, no. 4, 477 pages, 2003.
  123. P. Erixon, B. Svennblad, T. Britton, and B. Oxelman, “Reliability of Bayesian posterior probabilities and bootstrap frequencies in phylogenetics,” Systematic Biology, vol. 52, no. 5, 665 pages, 2003.
  124. B. Svennblad, P. Erixon, B. Oxelman, and T. Britton, “Fundamental differences between the methods of maximum likelihood and maximum posterior probability in phylogenetics,” Systematic Biology, vol. 55, no. 1, 116 pages, 2006.
  125. J. P. Huelsenbeck and B. Rannala, “Frequentist properties of Bayesian posterior probabilities of phylogenetic trees under simple and complex substitution models,” Systematic Biology, vol. 53, no. 6, 904 pages, 2004.
  126. P. O. Lewis, M. T. Holder, and K. E. Holsinger, “Polytomies and Bayesian phylogenetic inference,” Systematic Biology, vol. 54, no. 2, 241 pages, 2005.
  127. B. Kolaczkowski and J. W. Thornton, “Effects of branch length uncertainty on Bayesian posterior probabilities for phylogenetic hypotheses,” Molecular Biology and Evolution, vol. 24, no. 9, 2108 pages, 2007.
  128. M. Steel and F. A. Matsen, “The Bayesian “star paradox” persists for long finite sequences,” Molecular Biology and Evolution, vol. 24, no. 4, 1075 pages, 2007.
  129. Z. Yang, “Fair-balance paradox, star-tree paradox, and Bayesian phylogenetics,” Molecular Biology and Evolution, vol. 24, no. 8, 1639 pages, 2007.
  130. B. Kolaczkowski and J. W. Thornton, “Is there a star tree paradox?,” Molecular Biology and Evolution, vol. 23, no. 10, 1819 pages, 2006.
  131. E. Mossel and E. Vigoda, “Phylogenetic MCMC algorithms are misleading on mixtures of trees,” Science, vol. 309, no. 5744, 2207 pages, 2005.
  132. F. Ronquist, B. Larget, J. P. Huelsenbeck, J. B. Kadane, D. Simon, and P. van der Mark, “Comment on “Phylogenetic MCMC algorithms are misleading on mixtures of trees”,” Science, vol. 312, no. 5772, 367 pages, 2006.
  133. W. C. Wheeler and K. M. Pickett, “Topology-Bayes versus clade-Bayes in phylogenetic analysis,” Molecular Biology and Evolution, vol. 25, no. 2, 447 pages, 2008.
  134. B. Chor and T. Tuller, “Maximum likelihood of evolutionary trees: hardness and approximation,” Bioinformatics, vol. 21, supplement 1, i97 pages, 2005.
  135. M. J. Donoghue, “Progress and prospects in reconstructing plant phylogeny,” Annals of the Missouri Botanical Garden, vol. 81, no. 3, 405 pages, 1994.
  136. S. Aris-Brosou, “Least and most powerful phylogenetic tests to elucidate the origin of the seed plants in the presence of conflicting signals under misspecified models,” Systematic Biology, vol. 52, no. 6, 781 pages, 2003.
  137. H. Kishino and M. Hasegawa, “Evaluation of the maximum likelihood estimate of the evolutionary tree topologies from DNA sequence data, and the branching order in hominoide,” Journal of Molecular Evolution, vol. 29, no. 2, 170 pages, 1989.
  138. N. Goldman, J. P. Anderson, and A. G. Rodrigo, “Likelihood-based tests of topologies in phylogenetics,” Systematic Biology, vol. 49, no. 4, 652 pages, 2000.
  139. H. Shimodaira and M. Hasegawa, “Multiple comparisons of log-likelihoods with applications to phylogenetic inference,” Molecular Biology and Evolution, vol. 16, no. 8, 1114 pages, 1999.
  140. H. Shimodaira, “An approximately unbiased test of phylogenetic tree selection,” Systematic Biology, vol. 51, no. 3, 492 pages, 2002.
  141. S. Aris-Brosou, “How Bayes tests of molecular phylogenies compare with frequentist approaches,” Bioinformatics, vol. 19, no. 5, 618 pages, 2003.
  142. A. E. Raftery, “Hypothesis testing and model selection,” in Markov Chain Monte Carlo in Practice, W. Gilks, S. Richardson, and D. J. Spiegelhalter, Eds., p. 163, Chapman & Hall, Boca Raton, Fla, USA, 1996.
  143. J. A. A. Nylander, F. Ronquist, J. P. Huelsenbeck, and J. L. Nieves-Aldrey, “Bayesian phylogenetic analysis of combined data,” Systematic Biology, vol. 53, no. 1, 47 pages, 2004.
  144. S. C. Choi, A. Hobolth, D. M. Robinson, H. Kishino, and J. L. Thorne, “Quantifying the impact of protein tertiary structure on molecular evolution,” Molecular Biology and Evolution, vol. 24, no. 8, 1769 pages, 2007.
  145. S. Chib and I. Jeliazkov, “Marginal likelihood from the Metropolis-Hastings output,” Journal of the American Statistical Association, vol. 96, no. 453, 270 pages, 2001.
  146. N. Goldman, “Statistical tests of models of DNA substitution,” Journal of Molecular Evolution, vol. 36, no. 2, 182 pages, 1993.
  147. Z. Yang, Computational Molecular Evolution, Oxford University Press, Oxford, UK, 2006.
  148. J. Felsenstein, “Cases in which parsimony or compatibility methods will be positively misleading,” Systematic Zoology, vol. 27, no. 4, 401 pages, 1978.
  149. Z. Yang, “Maximum-likelihood models for combined analyses of multiple sequence data,” Journal of Molecular Evolution, vol. 42, no. 5, 587 pages, 1996.
  150. J. P. Huelsenbeck and M. A. Suchard, “A nonparametric method for accommodating and testing across-site rate variation,” Systematic Biology, vol. 56, no. 6, 975 pages, 2007.
  151. N. Lartillot and H. Philippe, “A Bayesian mixture model for across-site heterogeneities in the amino-acid replacement process,” Molecular Biology and Evolution, vol. 21, no. 6, 1095 pages, 2004.
  152. P. Lopez, D. Casane, and H. Philippe, “Heterotachy, an important process of protein evolution,” Molecular Biology and Evolution, vol. 19, no. 1, 1 pages, 2002.
  153. Z. Yang and D. Roberts, “On the use of nucleic acid sequences to infer early branchings in the tree of life,” Molecular Biology and Evolution, vol. 12, no. 3, 451 pages, 1995.
  154. W. M. Fitch and E. Markowitz, “An improved method for determining codon variability in a gene and its application to the rate of fixation of mutations in evolution,” Biochemical Genetics, vol. 4, no. 5, 579 pages, 1970.
  155. C. Tuffley and M. Steel, “Modeling the covarion hypothesis of nucleotide substitution,” Mathematical Biosciences, vol. 147, no. 1, 63 pages, 1998.
  156. J. P. Huelsenbeck, “Testing a covariotide model of DNA substitution,” Molecular Biology and Evolution, vol. 19, no. 5, 698 pages, 2002.
  157. B. Kolaczkowski and J. W. Thornton, “Performance of maximum parsimony and likelihood phylogenetics when evolution is heterogenous,” Nature, vol. 431, no. 7011, 980 pages, 2004.
  158. M. Spencer, E. Susko, and A. J. Roger, “Likelihood, parsimony, and heterogeneous evolution,” Molecular Biology and Evolution, vol. 22, no. 5, 1161 pages, 2005.
  159. N. Lartillot, H. Brinkmann, and H. Philippe, “Suppression of long-branch attraction artefacts in the animal phylogeny using a site-heterogeneous model,” BMC Evolutionary Biology, vol. 7, supplement 1, S4 pages, 2007.
  160. E. Jiménez-Guri, H. Philippe, B. Okamura, and P. W. H. Holland, “Buddenbrockia is a cnidarian worm,” Science, vol. 317, no. 5834, 116 pages, 2007.
  161. H. Philippe, Y. Zhou, H. Brinkmann, N. Rodrigue, and F. Delsuc, “Heterotachy and long-branch attraction in phylogenetics,” BMC Evolutionary Biology, vol. 5, article 50, 1 pages, 2005.
  162. M. Schöniger and A. Von Haeseler, “A stochastic model for the evolution of autocorrelated DNA sequences,” Molecular Phylogenetics and Evolution, vol. 3, no. 3, 240 pages, 1994.
  163. S. V. Muse and B. S. Gaut, “A likelihood approach for comparing synonymous and nonsynonymous nucleotide substitution rates, with application to the chloroplast genome,” Molecular Biology and Evolution, vol. 11, no. 5, 715 pages, 1994.
  164. N. Goldman and Z. Yang, “A codon-based model of nucleotide substitution for protein-coding DNA sequences,” Molecular Biology and Evolution, vol. 11, no. 5, 725 pages, 1994.
  165. A. Siepel and D. Haussler, “Phylogenetic estimation of context-dependent substitution rates by maximum likelihood,” Molecular Biology and Evolution, vol. 21, no. 3, 468 pages, 2004.
  166. D. G. Hwang and P. Green, “Bayesian Markov chain Monte Carlo sequence analysis reveals varying neutral substitution patterns in mammalian evolution,” Proceedings of the National Academy of Sciences of the United States of America, vol. 101, no. 39, 13994 pages, 2004.
  167. O. F. Christensen, A. Hobolth, and J. L. Jensen, “Pseudo-likelihood analysis of codon substitution models with neighbor-dependent rates,” Journal of Computational Biology, vol. 12, no. 9, 1166 pages, 2005.
  168. D. M. Robinson, D. T. Jones, H. Kishino, N. Goldman, and J. L. Thorne, “Protein evolution with dependence among codons due to tertiary structure,” Molecular Biology and Evolution, vol. 20, no. 10, 1692 pages, 2003.
  169. N. Rodrigue, N. Lartillot, D. Bryant, and H. Philippe, “Site interdependence attributed to tertiary structure in amino acid sequence evolution,” Gene, vol. 347, no. 2, 207 pages, 2005.
  170. N. Rodrigue, H. Philippe, and N. Lartillot, “Assessing site-interdependent phylogenetic models of sequence evolution,” Molecular Biology and Evolution, vol. 23, no. 9, 1762 pages, 2006.
  171. C. L. Kleinman, N. Rodrigue, C. Bonnard, H. Philippe, and N. Lartillot, “A maximum likelihood framework for protein design,” BMC Bioinformatics, vol. 7, article 326, 1 pages, 2006.
  172. A. Sato, H. Tichy, C. O'Huigin, P. R. Grant B, R. Grant, and J. Klein, “On the origin of Darwin's finches,” Molecular Biology and Evolution, vol. 18, no. 3, 299 pages, 2001.
  173. W. Salzburger, T. Mack, E. Verheyen, and A. Meyer, “Out of Tanganyika: genesis, explosive speciation, key-innovations and phylogeography of the haplochromine cichlid fishes,” BMC Evolutionary Biology, vol. 5, article 17, 1 pages, 2005.
  174. A. L. Hughes, “Looking for Darwin in all the wrong places: the misguided quest for positive selection at the nucleotide sequence level,” Heredity, vol. 99, no. 4, 364 pages, 2007.
  175. M. Kimura, The Neutral Theory of Molecular Evolution, Cambridge University Press, New York, NY, USA, 1983.
  176. M. Lynch, The Origins of Genome Architecture, Sinauer Associates, Sunderland, Mass, USA, 2007.
  177. R. Nielsen, “Statistical tests of selective neutrality in the age of genomics,” Heredity, vol. 86, no. 6, 641 pages, 2001.
  178. S. Aris-Brosou and L. Excoffier, “The impact of population expansion and mutation rate heterogeneity on DNA sequence polymorphism,” Molecular Biology and Evolution, vol. 13, no. 3, 494 pages, 1996.
  179. C. D. Bustamante, J. Wakeley, S. Sawyer, and D. L. Hartl, “Directional selection and the site-frequency spectrum,” Genetics, vol. 159, no. 4, 1779 pages, 2001.
  180. L. Zhu and C. D. Bustamante, “A composite-likelihood approach for detecting directional selection from DNA sequence data,” Genetics, vol. 170, no. 3, 1411 pages, 2005.
  181. M. Bamshad and S. P. Wooding, “Signatures of natural selection in the human genome,” Nature Reviews Genetics, vol. 4, no. 2, 99 pages, 2003.
  182. M. Anisimova and D. A. Liberles, “The quest for natural selection in the age of comparative genomics,” Heredity, vol. 99, no. 6, 567 pages, 2007.
  183. M. Nei and T. Gojobori, “Simple methods for estimating the numbers of synonymous and nonsynonymous nucleotide substitutions,” Molecular Biology and Evolution, vol. 3, no. 5, 418 pages, 1986.
  184. W. S. W. Wong and R. Nielsen, “Detecting selection in noncoding regions of nucleotide sequences,” Genetics, vol. 167, no. 2, 949 pages, 2004.
  185. S. McCauley, S. de Groot, T. Mailund, and J. Hein, “Annotation of selection strengths in viral genomes,” Bioinformatics, vol. 23, no. 22, 2978 pages, 2007.
  186. Z. Yang, “Adaptive molecular evolution,” in Handbook of Statistical Genetics, D. J. Balding, M. Bishop, and C. Cannings, Eds., p. 229, John Wiley & Sons, New York, NY, USA, 2nd edition, 2003.
  187. Z. Yang and R. Nielsen, “Estimating synonymous and nonsynonymous substitution rates under realistic evolutionary models,” Molecular Biology and Evolution, vol. 17, no. 1, 32 pages, 2000.
  188. W. S. W. Wong, Z. Yang, N. Goldman, and R. Nielsen, “Accuracy and power of statistical methods for detecting adaptive evolution in protein coding sequences and for identifying positively selected sites,” Genetics, vol. 168, no. 2, 1041 pages, 2004.
  189. J. Zhang, R. Nielsen, and Z. Yang, “Evaluation of an improved branch-site likelihood method for detecting positive selection at the molecular level,” Molecular Biology and Evolution, vol. 22, no. 12, 2472 pages, 2005.
  190. J. Zhang, S. Kumar, and M. Nei, “Small-sample tests of episodic adaptive evolution: a case study of primate lysozymes,” Molecular Biology and Evolution, vol. 14, no. 12, 1335 pages, 1997.
  191. Z. Yang, “Likelihood ratio tests for detecting positive selection and application to primate lysozyme evolution,” Molecular Biology and Evolution, vol. 15, no. 5, 568 pages, 1998.
  192. R. Nielsen and Z. Yang, “Likelihood models for detecting positively selected amino acid sites and applications to the HIV-1 envelope gene,” Genetics, vol. 148, no. 3, 929 pages, 1998.
  193. Y. Suzuki and T. Gojobori, “A method for detecting positive selection at single amino acid sites,” Molecular Biology and Evolution, vol. 16, no. 10, 1315 pages, 1999.
  194. Z. Yang, R. Nielsen, N. Goldman, and A.-M. K. Pedersen, “Codon-substitution models for heterogeneous selection pressure at amino acid sites,” Genetics, vol. 155, no. 1, 431 pages, 2000.
  195. T. Massingham and N. Goldman, “Detecting amino acid sites under positive selection and purifying selection,” Genetics, vol. 169, no. 3, 1753 pages, 2005.
  196. S. L. Kosakovsky Pond and S. D. W. Frost, “Not so different after all: a comparison of methods for detecting amino acid sites under selection,” Molecular Biology and Evolution, vol. 22, no. 5, 1208 pages, 2005.
  197. Z. Yang and R. Nielsen, “Codon-substitution models for detecting molecular adaptation at individual sites along specific lineages,” Molecular Biology and Evolution, vol. 19, no. 6, 908 pages, 2002.
  198. M. Anisimova and Z. Yang, “Molecular evolution of the hepatitis delta virus antigen gene: recombination or positive selection?,” Journal of Molecular Evolution, vol. 59, no. 6, 815 pages, 2004.
  199. S. Aris-Brosou, “Determinants of adaptive evolution at the molecular level: the extended complexity hypothesis,” Molecular Biology and Evolution, vol. 22, no. 2, 200 pages, 2005.
  200. M. Anisimova, J. P. Bielawski, and Z. Yang, “Accuracy and power of Bayes prediction of amino acid sites under positive selection,” Molecular Biology and Evolution, vol. 19, no. 6, 950 pages, 2002.
  201. Z. Yang, W. S. W. Wong, and R. Nielsen, “Bayes empirical Bayes inference of amino acid sites under positive selection,” Molecular Biology and Evolution, vol. 22, no. 4, 1107 pages, 2005.
  202. J. P. Huelsenbeck and K. A. Dyer, “Bayesian estimation of positively selected sites,” Journal of Molecular Evolution, vol. 58, no. 6, 661 pages, 2004.
  203. S. Aris-Brosou, “Identifying sites under positive selection with uncertain parameter estimates,” Genome, vol. 49, no. 7, 767 pages, 2006.
  204. M. Anisimova, R. Nielsen, and Z. Yang, “Effect of recombination on the accuracy of the likelihood method for detecting positive selection at amino acid sites,” Genetics, vol. 164, no. 3, 1229 pages, 2003.
  205. M. Anisimova, J. Bielawski, K. Dunn, and Z. Yang, “Phylogenomic analysis of natural selection pressure in Streptococcus genomes,” BMC Evolutionary Biology, vol. 7, article 154, 1 pages, 2007.
  206. E. Zuckerkandl and L. Pauling, “Molecules as documents of evolutionary history,” Journal of Theoretical Biology, vol. 8, no. 2, 357 pages, 1965.
  207. E. Zuckerkandl and L. Pauling, “Evolutionary divergence and convergence in proteins,” in Evolving Genes and Proteins, V. Bryson and H. J. Vogel, Eds., Academic Press, New York, NY, USA, 1965.
  208. L. Bromham and D. Penny, “The modern molecular clock,” Nature Reviews Genetics, vol. 4, no. 3, 216 pages, 2003.
  209. S. Aris-Brosou, “Dating phylogenies with hybrid local molecular clocks,” PLoS ONE, vol. 2, no. 9, e879 pages, 2007.
  210. H. Kishino and M. Hasegawa, “Converting distance to time: application to human evolution,” Methods in Enzymology, vol. 183, 550 pages, 1990.
  211. A. Rambaut and L. Bromham, “Estimating divergence dates from molecular sequences,” Molecular Biology and Evolution, vol. 15, no. 4, 442 pages, 1998.
  212. A. D. Yoder and Z. Yang, “Estimation of primate speciation dates using local molecular clocks,” Molecular Biology and Evolution, vol. 17, no. 7, 1081 pages, 2000.
  213. Z. Yang and A. D. Yoder, “Comparison of likelihood and Bayesian methods for estimating divergence times using multiple gene loci and calibration points, with application to a radiation of cute-looking mouse Lemur species,” Systematic Biology, vol. 52, no. 5, 705 pages, 2003.
  214. Z. Yang, “A heuristic rate smoothing procedure for maximum likelihood estimation of species divergence times,” Acta Zoologica Sinica, vol. 50, 645 pages, 2004.
  215. M. J. Sanderson, “Estimating absolute rates of molecular evolution and divergence times: a penalized likelihood approach,” Molecular Biology and Evolution, vol. 19, no. 1, 101 pages, 2002.
  216. A. B. Smith, D. Pisani, J. A. Mackenzie-Dodds, B. Stockley, B. L. Webster, and D. T. J. Littlewood, “Testing the molecular clock: molecular and paleontological estimates of divergence times in the Echinoidea (Echinodermata),” Molecular Biology and Evolution, vol. 23, no. 10, 1832 pages, 2006.
  217. M. J. Sanderson, “A nonparametric approach to estimating divergence times in the absence of rate constancy,” Molecular Biology and Evolution, vol. 14, no. 12, 1218 pages, 1997.
  218. S. Aris-Brosou and Z. Yang, “Effects of models of rate evolution on estimation of divergence dates with special reference to the metazoan 18S ribosomal RNA phylogeny,” Systematic Biology, vol. 51, no. 5, 703 pages, 2002.
  219. S. Aris-Brosou and Z. Yang, “Bayesian models of episodic evolution support a late Precambrian explosive diversification of the Metazoa,” Molecular Biology and Evolution, vol. 20, no. 12, 1947 pages, 2003.
  220. S. Y. Ho, M. J. Phillips, A. J. Drummond, and A. Cooper, “Accuracy of rate estimation using relaxed-clock models with a critical focus on the early metazoan radiation,” Molecular Biology and Evolution, vol. 22, no. 5, 1355 pages, 2005.
  221. J. J. Welch, E. Fontanillas, and L. Bromham, “Molecular dates for the “cambrian explosion”: the influence of prior assumptions,” Systematic Biology, vol. 54, no. 4, 672 pages, 2005.
  222. M. Aitkin, “Posterior Bayes factors,” Journal of the Royal Statistical Society B, vol. 53, no. 1, 111 pages, 1991.
  223. A. J. Drummond, S. Y. Ho, M. J. Phillips, and A. Rambaut, “Relaxed phylogenetics and dating with confidence,” PLoS Biology, vol. 4, no. 5, e88 pages, 2006.
  224. J. P. Huelsenbeck, J. P. Bollback, and A. M. Levine, “Inferring the root of a phylogenetic tree,” Systematic Biology, vol. 51, no. 1, 32 pages, 2002.
  225. J. Shendure, R. D. Mitra, C. Varma, and G. M. Church, “Advanced sequencing technologies: methods and goals,” Nature Reviews Genetics, vol. 5, no. 5, 335 pages, 2004.
  226. M. J. Moore, A. Dhingra, P. S. Soltis, et al., “Rapid and accurate pyrosequencing of angiosperm plastid genomes,” BMC Plant Biology, vol. 6, article 17, 1 pages, 2006.
  227. P. Green, “2x genomes—Does depth matter?,” Genome Research, vol. 17, no. 11, 1547 pages, 2007.
  228. A. Rokas, B. L. Williams, N. King, and S. B. Carroll, “Genome-scale approaches to resolving incongruence in molecular phylogenies,” Nature, vol. 425, no. 6960, 798 pages, 2003.
  229. A. G. Clark, M. B. Eisen, D. R. Smith, et al., “Evolution of genes and genomes on the Drosophila phylogeny,” Nature, vol. 450, no. 7167, 203 pages, 2007.
  230. F. Delsuc, H. Brinkmann, and H. Philippe, “Phylogenomics and the reconstruction of the tree of life,” Nature Reviews Genetics, vol. 6, no. 5, 361 pages, 2005.
  231. F. Ge, L. S. Wang, and J. Kim, “The cobweb of life revealed by genome-scale estimates of horizontal gene transfer,” PLoS Biology, vol. 3, no. 10, e316 pages, 2005.
  232. R. D. M. Page, “Extracting species trees from complex gene trees: reconciled trees and vertebrate phylogeny,” Molecular Phylogenetics and Evolution, vol. 14, no. 1, 89 pages, 2000.
  233. M. J. Phillips, F. Delsuc, and D. Penny, “Genome-scale phylogeny and the detection of systematic biases,” Molecular Biology and Evolution, vol. 21, no. 7, 1455 pages, 2004.
  234. H. Nishihara, N. Okada, and M. Hasegawa, “Rooting the eutherian tree: the power and pitfalls of phylogenomics,” Genome Biology, vol. 8, no. 9, R199 pages, 2007.
  235. N. Rodríguez-Ezpeleta, H. Brinkmann, B. Roure, N. Lartillot, B. F. Lang, and H. Philippe, “Detecting and overcoming systematic errors in genome-scale phylogenies,” Systematic Biology, vol. 56, no. 3, 389 pages, 2007.
  236. S. B. Hedges, J. Dudley, and S. Kumar, “TimeTree: a public knowledge-base of divergence times among organisms,” Bioinformatics, vol. 22, no. 23, 2971 pages, 2006.
  237. J. E. Janečka, W. Miller, T. H. Pringle, et al., “Molecular and genomic data identify the closest living relative of primates,” Science, vol. 318, no. 5851, 792 pages, 2007.
  238. S. Kumar and J. Dudley, “Bioinformatics software for biologists in the genomics era,” Bioinformatics, vol. 23, no. 14, 1713 pages, 2007.