Journal of Molecular Evolution

, Volume 25, Issue 4, pp 351–360

Progressive sequence alignment as a prerequisitetto correct phylogenetic trees

  • Da-Fei Feng
  • Russell F. Doolittle

DOI: 10.1007/BF02603120

Cite this article as:
Feng, DF. & Doolittle, R.F. J Mol Evol (1987) 25: 351. doi:10.1007/BF02603120


A progressive alignment method is described that utilizes the Needleman and Wunsch pairwise alignment algorithm iteratively to achieve the multiple alignment of a set of protein sequences and to construct an evolutionary tree depicting their relationship. The sequences are assumed a priori to share a common ancestor, and the trees are constructed from difference matrices derived directly from the multiple alignment. The thrust of the method involves putting more trust in the comparison of recently diverged sequences than in those evolved in the distant past. In particular, this rule is followed: “once a gap, always a gap”. The method has been applied to three sets of protein sequences: 7 superoxide dismutases, 11 globins, and 9 tyrosine kinase-like sequences. Multiple alignments and phylogenetic trees for these sets of sequences were determined and compared with trees derived by conventional pairwise treatments. In several instances, the progressive method led to trees that appeared to be more in line with biological expectations than were trees obtained by more commonly used methods.

Key words

Multiple sequence alignmentsEvolutionary trees

Copyright information

© Springer-Verlag New York Inc. 1987

Authors and Affiliations

  • Da-Fei Feng
    • 1
  • Russell F. Doolittle
    • 1
  1. 1.Department of ChemistryUniversity of California-San DiegoLa JollaUSA