A novel approach to phylogeny reconstruction from protein sequences

Research output: Contribution to journalArticle

8 Citations (Scopus)

Abstract

The reliable reconstruction of tree topology from a set of homologous sequences is one of the main goals in the study of molecular evolution. If consistent estimators of distances from a multiple sequence alignment are known, the distance method is attractive because the tree reconstruction is consistent. To obtain a distance estimate d, the observed proportion of differences p (p-distance) is usually 'corrected' for multiple and back substitutions by means of a functional relationship d = f(p). In this paper the conditions under which this correction of p-distances will not alter the selection of the tree topology are specified. When these conditions are not fulfilled the selection of the tree topology may depend on the correction function applied. A novel method which includes estimates of distances not only between sequence pairs, but between triplets, quadruplets, etc., is proposed to strengthen the proper selection of correction function and tree topology. A 'super' tree that includes all tree topologies as special cases is introduced.

Original languageEnglish (US)
Pages (from-to)264-273
Number of pages10
JournalJournal of Molecular Evolution
Volume48
Issue number3
StatePublished - 1999

Fingerprint

Phylogeny
topology
Trees (mathematics)
phylogeny
amino acid sequences
Topology
protein
Molecular Evolution
Sequence Alignment
Sequence Homology
Proteins
sequence alignment
sequence homology
substitution
Substitution reactions
methodology
method

Keywords

  • Amniote phylogeny
  • Evolutionary distance
  • Phylogenetic tree
  • Substitution rates

ASJC Scopus subject areas

  • Genetics
  • Biochemistry
  • Biochemistry, Genetics and Molecular Biology(all)
  • Genetics(clinical)
  • Ecology, Evolution, Behavior and Systematics
  • Molecular Biology
  • Agricultural and Biological Sciences(all)
  • Agricultural and Biological Sciences (miscellaneous)

Cite this

A novel approach to phylogeny reconstruction from protein sequences. / Grishin, Nick V.

In: Journal of Molecular Evolution, Vol. 48, No. 3, 1999, p. 264-273.

Research output: Contribution to journalArticle

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