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Inference of phylogenetic distances from DNA-walk divergences

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  • Licinio, P
  • Caligiorne, R.B

Abstract

A formalism for the analysis of DNA-sequences is presented. It develops the concept of a composition vector potential which incorporates intrinsic double-strand and four-base symmetries. The vector potential allows for straightforward coarse graining and graphical representation of whole genomes. Its projections are mapped onto DNA-walks. It is shown that distances due to mutation between sequences can be estimated from mean square differences between walks. A computer program for global alignment of sequences (DNAWD) is thus developed and applied to a set of toy sequences representing evolution under mutation. The distance matrix output of DNAWD is shown to provide a good estimate of the associated phylogenetic tree.

Suggested Citation

  • Licinio, P & Caligiorne, R.B, 2004. "Inference of phylogenetic distances from DNA-walk divergences," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 341(C), pages 471-481.
    • Handle: RePEc:eee:phsmap:v:341:y:2004:i:c:p:471-481
    DOI: 10.1016/j.physa.2004.03.098
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    References listed on IDEAS

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    1. Buldyrev, S.V. & Dokholyan, N.V. & Goldberger, A.L. & Havlin, S. & Peng, C.-K. & Stanley, H.E. & Viswanathan, G.M., 1998. "Analysis of DNA sequences using methods of statistical physics," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 249(1), pages 430-438.
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    5. Stanley, H.E & Buldyrev, S.V & Goldberger, A.L & Havlin, S & Peng, C.-K & Simons, M, 1999. "Scaling features of noncoding DNA," Physica A: Statistical Mechanics and its Applications, Elsevier, vol. 273(1), pages 1-18.
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