Generation of hierarchically correlated multivariate symbolic sequences: With an application to the assessment of bootstrap confidence in phylogenetic analysis.

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1 Citazioni (Scopus)

Abstract

We introduce a method to generate multivariate series of symbols from a finite alphabet with agiven hierarchical structure of similarities based on the Hamming distance. The target hierarchical structureof similarities is arbitrary, for instance the one obtained by some hierarchical clustering method applied toan empirical matrix of similarities. The method that we present here is based on a generating mechanismthat does not make use of mutation rate, which is widely used in phylogenetic analysis. Here we use theproposed simulation method to investigate the relationship between the bootstrap value associated witha node of a phylogeny and the probability of finding that node in the true phylogeny. The results of thisanalysis are compared with those obtained in the literature according to an evolutionary model with aper-symbol constant mutation rate. We observe that the relationship between the bootstrap value of anode and the probability of the corresponding clade being correct is sensitive to both the length of dataseries and the length of the branch connecting the node to its closest ancestor in the phylogenetic tree,whereas such a relationship is only slightly affected by the topology of the true phylogeny and by theabsolute value of similarity.
Lingua originaleEnglish
pagine (da-a)333-340
Numero di pagine8
RivistaTHE EUROPEAN PHYSICAL JOURNAL. B, CONDENSED MATTER PHYSICS
Volume2008
Stato di pubblicazionePublished - 2008

All Science Journal Classification (ASJC) codes

  • Electronic, Optical and Magnetic Materials
  • Condensed Matter Physics

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