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Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction

Author

Listed:
  • Bin Ma

    (University of Waterloo)

  • Louxin Zhang

    (National University of Singapore)

Abstract

The marginal maximum likelihood method is a widely-used method for ancestral state reconstruction. Given an evolution model (a phylogeny tree and the edge mutation rates) and the extant states (states on leaves), the method computes efficiently the most likely ancestral state on the root. However, when the extant states are randomly generated by using the evolutionary model, it is unknown how to efficiently calculate the expected reconstruction accuracy of the marginal maximum likelihood method. In this paper, a fully polynomial time approximation scheme (FPTAS) is presented for the calculation.

Suggested Citation

  • Bin Ma & Louxin Zhang, 2011. "Efficient estimation of the accuracy of the maximum likelihood method for ancestral state reconstruction," Journal of Combinatorial Optimization, Springer, vol. 21(4), pages 409-422, May.
    • Handle: RePEc:spr:jcomop:v:21:y:2011:i:4:d:10.1007_s10878-009-9261-6
    DOI: 10.1007/s10878-009-9261-6
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    References listed on IDEAS

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    1. Eric A. Gaucher & J. Michael Thomson & Michelle F. Burgan & Steven A. Benner, 2003. "Inferring the palaeoenvironment of ancient bacteria on the basis of resurrected proteins," Nature, Nature, vol. 425(6955), pages 285-288, September.
    2. Paul D Williams & David D Pollock & Benjamin P Blackburne & Richard A Goldstein, 2006. "Assessing the Accuracy of Ancestral Protein Reconstruction Methods," PLOS Computational Biology, Public Library of Science, vol. 2(6), pages 1-8, June.
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    Cited by:

    1. Zhi-Zhong Chen & Ying Fan & Lusheng Wang, 2015. "Faster exact computation of rSPR distance," Journal of Combinatorial Optimization, Springer, vol. 29(3), pages 605-635, April.

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