Inference of phylogenetic distances from DNA-walk divergences

P Licinio and R.b Caligiorne

Physica A: Statistical Mechanics and its Applications, 2004, vol. 341, issue C, 471-481

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.

Keywords: DNA-walk; Phylogenetics; Global alignment; Composition potential (search for similar items in EconPapers)
Date: 2004
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:341:y:2004:i:c:p:471-481

DOI: 10.1016/j.physa.2004.03.098

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