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Updated: May 12, 2026

A Practical Guide to Phylogenetics for Nonexperts
Published on: February 5, 2014
Non-degenerate graphical representation of DNA sequences and its applications to phylogenetic analysis
Yan Yang1, Yingying Zhang, Meiduo Jia
1Department of Mathematics, Bohai University, Jinzhou 121013, P.R. China.
Abstract:
In this paper, we propose a new 3-D graphical representation of a DNA sequence and prove that it has two properties: (1) there is no circuit in the graph; (2) there exists a one-to-one correspondence between a DNA sequence and the graph. These properties guarantee it has nondegeneracy. Based on the 3-D graphical representation, we characterize a DNA sequence by a 12-dimensional vector whose components are normalized ALE-indexes of the corresponding L/L matrices. The proposed approach is tested by the phylogenetic analysis on three datasets, and the experimental assessment demonstrates its efficiency.
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