Journal of South China University of Technology(Natural Science Edition) ›› 2019, Vol. 47 ›› Issue (6): 136-141,148.doi: 10.12141/j.issn.1000-565X.180313

• Biotechnology • Previous Articles     Next Articles

Feasibility Evaluation of Dissimilarity Algorithm and Adjacency Method for Constructing Evolutionary Tree

LIU Xuemei LI Wen HUANG Guanda HUANG Tianlai YE Yuzhong XU Guohao    

  1. School of Physics and Optoelectronics，South China University of Technology，Guangzhou 510640，Guangdong，China 
  • Received:2018-11-21 Revised:2018-09-14 Online:2019-06-25 Published:2019-05-05
  • Contact: 刘雪梅(1975-)，女，博士，副教授，主要从事生物信息学研究． E-mail:liuxm@scut.edu.cn
  • About author:刘雪梅(1975-)，女，博士，副教授，主要从事生物信息学研究．
  • Supported by:
    Supported by the National Natural Science Foundation of China(11205061) and the Science and Technology Planning Project of Guangdong Province(2016A010101020) 

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Abstract: In phylogenetic，the algorithm of constructing evolutionary tree is the basis of studying evolutionary rela- tionship． The feasibility of constructing evolutionary tree based on k-mer dissimilarity algorithm d2S and adjacency method NJ was discussed and verified． The evolutionary tree was constructed for 12 16S rRNA and 36 bacterio- phage molecule sequences in two evolutionary scenarios (k =4，6，8，10)． Three types of 16S rRNA were clear- ly classified according to archaea，bacteria and eukaryotes，and the results are basically consistent with Woese cata- logue． At the same time，four types of bacteriophages can be distinguished according to the original evolutionary relationship，and the influence of parameter k is small，so the classification effect is very good． This demonstrates the powerful function of the dissimilarity algorithm d2S． Using the dissimilarity algorithm d2S and the adjacency method (NJ) to construct the evolutionary tree will provide a new algorithm and idea for the phylogenetic relation- ship of the system．

Key words: dissimilarity algorithm d2S, adjacency method (NJ), k-mer, 16S rRNA, bacteriophages’

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