Journal of Molecular Evolution

, Volume 53, Issue 6, pp 660–669

Assessing Variability by Joint Sampling of Alignments and Mutation Rates

  • Dirk  Metzler
  • Roland  Fleißner
  • Anton  Wakolbinger
  • Arndt  von Haeseler
Article

DOI: 10.1007/s002390010253

Cite this article as:
Metzler, D., Fleißner, R., Wakolbinger, A. et al. J Mol Evol (2001) 53: 660. doi:10.1007/s002390010253

Abstract

When two sequences are aligned with a single set of alignment parameters, or when mutation parameters are estimated on the basis of a single ``optimal'' sequence alignment, the variability of both the alignment and the estimated parameters can be seriously underestimated. To obtain a more realistic impression of the actual uncertainty, we propose sampling sequence alignments and mutation parameters simultaneously from their joint posterior distribution given the two original sequences. We illustrate our method with human and orangutan sequences from the hyper variable region I and with gene–pseudogene pairs.

Key words: Sequence alignment — Markov chain Monte Carlo method — Thorne–Kishino–Felsenstein modelMutation parameter estimation — Statistical alignment — Hypervariable region — Pseudogenes — Hidden Markov model

Copyright information

© Springer-Verlag New York Inc. 2001

Authors and Affiliations

  • Dirk  Metzler
    • 1
  • Roland  Fleißner
    • 2
  • Anton  Wakolbinger
    • 1
  • Arndt  von Haeseler
    • 2
  1. 1.Johann Wolfgang Goethe-Universität, Fachbereich Mathematik, D-60054 Frankfurt am Main, GermanyDE
  2. 2.Max-Planck-Institut für evolutionäre Anthropologie, Inselstraße 22, D-04103 Leipzig, GermanyDE