An Efficient Algorithm for Statistical Multiple Alignment on Arbitrary Phylogenetic Trees

G. A. Lunter, I. Miklós, Y. S. Song, J. Hein

Research output: Contribution to journalArticle

36 Citations (Scopus)


We present an efficient algorithm for statistical multiple alignment based on the TKF91 model of Thorne, Kishino, and Felsenstein (1991) on an arbitrary k-leaved phylogenetic tree. The existing algorithms use a hidden Markov model approach, which requires at least O (√5k) states and leads to a time complexity of O (5kLk), where L is the geometric mean sequence length. Using a combinatorial technique reminiscent of inclusion/exclusion, we are able to sum away the states, thus improving the time complexity to O (2kLk) and considerably reducing memory requirements. This makes statistical multiple alignment under the TKF91 model a definite practical possibility in the case of a phylogenetic tree with a modest number of leaves.

Original languageEnglish
Pages (from-to)869-889
Number of pages21
JournalJournal of Computational Biology
Issue number6
Publication statusPublished - Dec 1 2003



  • Maximum likelihood
  • Multiple alignment
  • Phylogeny
  • Statistical alignment

ASJC Scopus subject areas

  • Modelling and Simulation
  • Molecular Biology
  • Genetics
  • Computational Mathematics
  • Computational Theory and Mathematics

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