Fractal and Dynamical Language Methods to Construct Phylogenetic Tree Based on Protein Sequences from Complete Genomes

The complete genomes of living organisms have provided much information on their phylogenetic relationships. In the past few years, we proposed three alternative methods to model the noise background in the composition vector of protein sequences from a complete genome. The first method is based on the frequencies of the 20 kinds of amino acids appearing in the genome and the multiplicative model. The second method is based on the iterated function system model in fractal geometry. The last method is based on the relationship between a word and its two sub-words in the theory of symbolic dynamics. Here we introduce these methods. The complete genomes of prokaryotes and eukaryotes are selected to test these algorithms. Our distance-based phylogenetic tree of prokaryotes and eukaryotes agrees with the biologists' “tree of life” based on the 16S-like rRNA genes in a majority of basic branches and most lower taxa.

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