摘要
Composition vector trees （CVTrees） are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.
Composition vector trees （CVTrees） are inferred from whole-genome data by an alignment-free and parameter-free method. The agreement of these trees with the corresponding taxonomy provides an objective justification of the inferred phylogeny. In this work, we show the stability and self-consistency of CVTrees by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach. Our ultimate goal is to advocate the viewpoint that time-consuming statistical re-sampling tests can be avoided at all in using this alignment-free approach. Agreement with taxonomy should be taken as a major criterion to estimate prokaryotic phylogenetic trees.
作者
Guanghong Zuo1,2, Zhao Xu1,3, Hongjie Yu1,4, and Bailin Hao1,5,6 1T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China
2Shanghai Institute of Applied Physics, Chinese Acadamy of Sciences, Shanghai 201800, China
3Applied Biosystems, Inc., Beijing 100027, China
4Fudan-VARI Center for Genetic Epidemiology, Fudan University, Shanghai 200433, China
5Institute of Theoretical Physics, Chinese Acadamy of Sciences, Beijing 100190, China
6Santa Fe Institute, Santa Fe, NM 87505, USA.
基金
supported by the National Basic Research Program of China (the 973 Program, Grant No. 2007CB814800)
the Shanghai Leading Academic Discipline Project (Grant No. B111)
