Jackknife and Bootstrap Tests of the Composition Vector 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.

[1]  M. Nei,et al.  A Simple Method for Estimating and Testing Minimum-Evolution Trees , 1992 .

[2]  Hong Luo,et al.  CVTree: a phylogenetic tree reconstruction tool based on whole genomes , 2004, Nucleic Acids Res..

[3]  Lior Pachter,et al.  Why Neighbor-Joining Works , 2006, Algorithmica.

[4]  Zu-Guo Yu,et al.  Origin and phylogeny of chloroplasts revealed by a simple correlation analysis of complete genomes. , 2003, Molecular biology and evolution.

[5]  J. Qi,et al.  Whole genome molecular phylogeny of large dsDNA viruses using composition vector method , 2007, BMC Evolutionary Biology.

[6]  Zhao Xu,et al.  Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations. , 2010, Journal of biotechnology.

[7]  A. Oskooi.  Molecular Evolution and Phylogenetics , 2008 .

[8]  D. Penny,et al.  The Use of Tree Comparison Metrics , 1985 .

[9]  J. Qi,et al.  Whole Proteome Prokaryote Phylogeny Without Sequence Alignment: A K-String Composition Approach , 2003, Journal of Molecular Evolution.

[10]  D. Robinson,et al.  Comparison of phylogenetic trees , 1981 .

[11]  Zhao Xu,et al.  A fungal phylogeny based on 82 complete genomes using the composition vector method , 2009, BMC Evolutionary Biology.

[12]  GaoLei,et al.  Molecular phylogeny of coronaviruses including human SARS-CoV , 2003 .

[13]  Bailin Hao,et al.  Prokaryote phylogeny without sequence alignment: from avoidance signature to composition distance. , 2004, Journal of bioinformatics and computational biology.

[14]  Ji Qi,et al.  Prokaryote phylogeny meets taxonomy: An exhaustive comparison of composition vector trees with systematic bacteriology , 2007, Science in China Series C: Life Sciences.

[15]  N. Saitou,et al.  The neighbor-joining method: a new method for reconstructing phylogenetic trees. , 1987, Molecular biology and evolution.

[16]  Zhao Xu,et al.  CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes , 2009, Nucleic Acids Res..