PMID: 9541878May 16, 1998Paper

Evolution of DNA or amino acid sequences with dependent sites

Journal of Computational Biology : a Journal of Computational Molecular Cell Biology
A von Haeseler, M Schöniger

Abstract

A framework is outlined to study the evolution of DNA or amino acid sequences, if sequence sites do not evolve independently. The units of evolution are nonoverlapping subsequences of length l. Each subsequence evolves independently of the others, but within a subsequence the sequences show a Markov order one dependency. We describe an algorithm to mimic the evolution of such sequences. The influence of dependencies between sites on distance estimates and the reliability of tree reconstruction methods is investigated. We show that an inappropriate model of sequence evolution in the tree reconstruction process will lead to a nonempty Felsenstein zone. Finally, we describe a method to infer l from sequence data. Examples from the evolution of DNA sequences as well as from amino acids are given.

References

Mar 24, 1975·Journal of Molecular Evolution·R A Elton
Jan 1, 1987·Journal of Molecular Evolution·P J Avery
Jan 1, 1985·Journal of Molecular Evolution·M HasegawaT Yano
Jun 1, 1974·Journal of Theoretical Biology·R A Elton
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Sep 1, 1994·Molecular Phylogenetics and Evolution·M Schöniger, A von Haeseler
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Sep 1, 1994·Journal of Molecular Evolution·A Zharkikh
Apr 1, 1996·Journal of Molecular Evolution·J Adachi, M Hasegawa

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Citations

Feb 14, 2006·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Anna GambinJerzy Tyszkiewicz
Dec 8, 2005·Bioinformatics·Tanja Gesell, Arndt von Haeseler
Mar 3, 2012·Molecular Biology and Evolution·Tina KoestlerIngo Ebersberger
Feb 14, 2020·Journal of Computational Biology : a Journal of Computational Molecular Cell Biology·Gary LarsonScott Schmidler

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