AUTHOR=Wu Yao-Qun , Yu Zu-Guo , Tang Run-Bin , Han Guo-Sheng , Anh Vo V. 

TITLE=An Information-Entropy Position-Weighted K-Mer Relative Measure for Whole Genome Phylogeny Reconstruction

JOURNAL=Frontiers in Genetics

VOLUME=12

YEAR=2021

URL=https://www.frontiersin.org/journals/genetics/articles/10.3389/fgene.2021.766496

DOI=10.3389/fgene.2021.766496

ISSN=1664-8021

ABSTRACT=<p>Alignment methods have faced disadvantages in sequence comparison and phylogeny reconstruction due to their high computational costs in handling time and space complexity. On the other hand, alignment-free methods incur low computational costs and have recently gained popularity in the field of bioinformatics. Here we propose a new alignment-free method for phylogenetic tree reconstruction based on whole genome sequences. A key component is a measure called <italic>information-entropy position-weighted k-mer relative measure</italic> (IEPWRMkmer), which combines the position-weighted measure of <italic>k</italic>-mers proposed by our group and the information entropy of frequency of <italic>k</italic>-mers. The Manhattan distance is used to calculate the pairwise distance between species. Finally, we use the Neighbor-Joining method to construct the phylogenetic tree. To evaluate the performance of this method, we perform phylogenetic analysis on two datasets used by other researchers. The results demonstrate that the <italic>IEPWRMkmer</italic> method is efficient and reliable. The source codes of our method are provided at <ext-link ext-link-type="uri" xlink:href="https://github.com/" xmlns:xlink="http://www.w3.org/1999/xlink">https://github.com/</ext-link> wuyaoqun37/IEPWRMkmer.</p>