Journal of Molecular Evolution

, Volume 20, Issue 2, pp 175–186

The alignment of sets of sequences and the construction of phyletic trees: An integrated method

  • P. Hogeweg
  • B. Hesper
Article

DOI: 10.1007/BF02257378

Cite this article as:
Hogeweg, P. & Hesper, B. J Mol Evol (1984) 20: 175. doi:10.1007/BF02257378

Summary

In this paper we argue that the alignment of sets of sequences and the construction of phyletic trees cannot be treated separately. The concept of ‘good alignment’ is meaningless without reference to a phyletic tree, and the construction of phyletic trees presupposes alignment of the sequences.

We propose an integrated method that generates both an alignment of a set of sequences and a phyletic tree. In this method a putative tree is used to align the sequences and the alignment obtained is used to adjust the tree; this process is iterated. As a demonstration we apply the method to the analysis of the evolution of 5S rRNA sequences in prokaryotes.

Key words

Sequence alignment Phyletic trees Matrix methods Internode sequences Homology assessment Tree representation Prokaryotic 5S rRNA evolution 

Copyright information

© Springer-Verlag 1984

Authors and Affiliations

  • P. Hogeweg
    • 1
  • B. Hesper
    • 1
  1. 1.BioinformaticaUtrechtThe Netherlands

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