Assessing confidence in phylogenetic trees : bootstrap versus Markov chain Monte Carlo

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Recent implementations of Bayesian approaches are one of the largest advances in phylogenetic tree estimation in the last 10 years. Markov chain Monte Carlo (MCMC) is used in these new approaches to estimate the Bayesian posterior probability for each tree topology of interest. Our goal is to assess the confidence in the estimated tree (particularly in whether prespecified groups are monophyletic) using MCMC and to compare the Bayesian estimate of confidence to a bootstrap-based estimate of confidence. We compare the Bayesian posterior probability to the bootstrap probability for specified groups in two real sets of influenza sequences and two sets ... continued below

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9 p.

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Burr, Tom; Doak, J. E. (Justin E.); Gattiker, J. R. (James R.) & Stanbro, W. D. (William D.) January 1, 2002.

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Recent implementations of Bayesian approaches are one of the largest advances in phylogenetic tree estimation in the last 10 years. Markov chain Monte Carlo (MCMC) is used in these new approaches to estimate the Bayesian posterior probability for each tree topology of interest. Our goal is to assess the confidence in the estimated tree (particularly in whether prespecified groups are monophyletic) using MCMC and to compare the Bayesian estimate of confidence to a bootstrap-based estimate of confidence. We compare the Bayesian posterior probability to the bootstrap probability for specified groups in two real sets of influenza sequences and two sets of simulated sequences for our comparison. We conclude that the bootstrap estimate is adequate compared to the MCMC estimate except perhaps if the number of DNA sites is small.

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9 p.

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  • "Submitted to: 2002 International Conference on Mathematics and Engineering Techniques in Medicine and Biological Sciences, Las Vegas, Nevada, June 24-27, 2002"

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  • Report No.: LA-UR-02-5043
  • Grant Number: none
  • Office of Scientific & Technical Information Report Number: 976280
  • Archival Resource Key: ark:/67531/metadc934616

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  • January 1, 2002

Added to The UNT Digital Library

  • Nov. 13, 2016, 7:26 p.m.

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  • Dec. 12, 2016, 2:55 p.m.

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Burr, Tom; Doak, J. E. (Justin E.); Gattiker, J. R. (James R.) & Stanbro, W. D. (William D.). Assessing confidence in phylogenetic trees : bootstrap versus Markov chain Monte Carlo, article, January 1, 2002; United States. (digital.library.unt.edu/ark:/67531/metadc934616/: accessed May 26, 2018), University of North Texas Libraries, Digital Library, digital.library.unt.edu; crediting UNT Libraries Government Documents Department.