Phylogenetic analysis of DNA sequences based on fractional Fourier transform

Kun Qian and Yihui Luan

Physica A: Statistical Mechanics and its Applications, 2018, vol. 509, issue C, 795-808

Abstract: Phylogenetic analysis of molecular sequences for inferring evolutionary relationships is an essential problem in biology. In this paper, we make an extension of Power Spectrum Moments method based on discrete fractional Fourier transform for phylogenetic analysis. DNA sequences are first converted into numeric sequences, and discrete fractional Fourier transform is then used on these numeric sequences to compute power spectra. By extracting a new j th moment feature based on power spectra, distance matrix is constructed and phylogenetic tree is built. Moreover, we give a guideline for choosing an appropriate order p of discrete fractional Fourier transform through simulation strategy and Friedman test. Our method is tested on three real datasets. Comparing with the Power Spectrum Moments method based on discrete Fourier transform and d2∗ measure, the results of phylogenetic trees demonstrate that our method is more efficient in inferring biological relationships.

Keywords: Phylogenetic tree; Discrete fractional Fourier transform; Power spectrum moments; Sequence comparison (search for similar items in EconPapers)
Date: 2018
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Persistent link: https://EconPapers.repec.org/RePEc:eee:phsmap:v:509:y:2018:i:c:p:795-808

DOI: 10.1016/j.physa.2018.06.044

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