CVTree: A WHOLE-GENOME-BASED AND ALIGNMENT-FREE APPROACH TO MICROBIAL PHYLOGENY

Abstract

The number of sequenced genomes of Archaea, Bacteria, and Fungi accumulates rapidly. Several thousands genomes of these unicellular organisms will be available in a few years. Due to the extremely large difference in genome size and gene content it is difficult to use the traditional alignment-based method to infer phylogeny from the genomes. An alignment-free and whole-genome-based approach called CVTree has been developed and successfully applied to these organisms. As CVTree has been successfully applied to genomes of viruses, chloroplasts, Bacteria, Archaea and fungi, in this brief review we will mainly touch on some mathematical problems related to the foundation of the new approach, including a few yet unsolved problems, such as the violation of the triangular inequalities of the dissimilarity measure used in the CVTree method.

以多肽组分特异性和gc含量分类细菌的有效性分析

“…最近, 我国学者郝柏林课题组 [21] 提出利用全基 因组或蛋白质组中"n 聚体"(即寡核苷酸或多肽)的组 分特异性来确定生物亲缘关系. 这是一种非序列比 对方法, 能准确鉴定目前综合不同方法确定出的微 生物亲缘关系, 有效克服了原有方法的诸多限制, 引 起了广泛关注 [22][23][24][25][26][27][28] . n 聚体组分特异性的研究显示, 仅在 n 取值适当的情况下才能得到准确的生物亲缘 关系.…”