基于k-mer组分信息的系统发生树构建方法

随着越来越多基因组的测序完成，基于全基因组的非比对的系统发生分析已成为研究热点。不同的生物物种或个体基因组之间的核酸组分不完全相同。遗传语言-DNA序列的信息很大程度上反映在其k—mer频数中。基于基因组序列k-mer频数的系统发生树则从新的角度为我们提供物种之间的亲缘关系。本文定义基于k-mer，频数的信息参数，并用它表征基因组序列，计算不同基因组之间信息参数的距离，用邻接法对84个病毒构建了系统发生树，发现构建的系统发生树很大程度上与已有的系统发生树相吻合。

A method for constructing phylogenetic tree based on k-mer information

With the success in the sequencing of complete genomes, the phylogenetics analysis by alignment-free methods based on complete genomes has been a hot topic. The nucleotide composition is different across species or populations. The information in the genetic language-DNA can be reflected largely in its k-mer frequencies. The phylogenetic tree based on k-mer frequencies would provide us the evolutionary relation among organisms from a no- vel perspective. In this study, the genomes of 84 large viruses are characterized by an info~nation parameter, which is defined based on k-mer frequencies in the sequences; then the distances among the virus genomes are calculated and a phylogenetic tree is constructed for the viruses by using neighbor-joining method. The obtained phylogenetic tree is largely in agreement with the others＇ tree.