On the complexity of multiple sequence alignment

J Comput Biol. 1994 Winter;1(4):337-48. doi: 10.1089/cmb.1994.1.337.


We study the computational complexity of two popular problems in multiple sequence alignment: multiple alignment with SP-score and multiple tree alignment. It is shown that the first problem is NP-complete and the second is MAX SNP-hard. The complexity of tree alignment with a given phylogeny is also considered.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Algorithms*
  • Models, Theoretical*
  • Phylogeny
  • Sequence Alignment / methods*