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      Jackknife and Bootstrap Tests of the Composition Vector Trees

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          Abstract

          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.

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          Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach.

          Ji Qi, Xue-bin Wang, Bai-Xia Hao (2003)
          A systematic way of inferring evolutionary relatedness of microbial organisms from the oligopeptide content, i.e., frequency of amino acid K-strings in their complete proteomes, is proposed. The new method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. The only "parameter" in the method is the length K of the oligopeptides, which serves to tune the "resolution power" of the method. The topology of the trees converges with K increasing. Applied to a total of 109 organisms, including 16 Archaea, 87 Bacteria, and 6 Eukarya, it yields an unrooted tree that agrees with the biologists' "tree of life" based on SSU rRNA comparison in a majority of basic branchings, and especially, in all lower taxa.
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            CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes

            Zhao Xu, Bailin Hao (2009)
            The CVTree web server (http://tlife.fudan.edu.cn/cvtree) presented here is a new implementation of the whole genome-based, alignment-free composition vector (CV) method for phylogenetic analysis. It is more efficient and user-friendly than the previously published version in the 2004 web server issue of Nucleic Acids Research. The development of whole genome-based alignment-free CV method has provided an independent verification to the traditional phylogenetic analysis based on a single gene or a few genes. This new implementation attempts to meet the challenge of ever increasing amount of genome data and includes in its database more than 850 prokaryotic genomes which will be updated monthly from NCBI, and more than 80 fungal genomes collected manually from several sequencing centers. This new CVTree web server provides a faster and stable research platform. Users can upload their own sequences to find their phylogenetic position among genomes selected from the server's; inbuilt database. All sequence data used in a session may be downloaded as a compressed file. In addition to standard phylogenetic trees, users can also choose to output trees whose monophyletic branches are collapsed to various taxonomic levels. This feature is particularly useful for comparing phylogeny with taxonomy when dealing with thousands of genomes.
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              CVTree: a phylogenetic tree reconstruction tool based on whole genomes

              Ji Qi, Hong Luo, Bailin Hao (2004)
              Composition Vector Tree (CVTree) implements a systematic method of inferring evolutionary relatedness of microbial organisms from the oligopeptide content of their complete proteomes ( http://cvtree.cbi.pku.edu.cn ). Since the first bacterial genomes were sequenced in 1995 there have been several attempts to infer prokaryote phylogeny from complete genomes. Most of them depend on sequence alignment directly or indirectly and, in some cases, need fine-tuning and adjustment. The composition vector method circumvents the ambiguity of choosing the genes for phylogenetic reconstruction and avoids the necessity of aligning sequences of essentially different length and gene content. This new method does not contain ‘free’ parameter and ‘fine-tuning’. A bootstrap test for a phylogenetic tree of 139 organisms has shown the stability of the branchings, which support the small subunit ribosomal RNA (SSU rRNA) tree of life in its overall structure and in many details. It may provide a quick reference in prokaryote phylogenetics whenever the proteome of an organism is available, a situation that will become commonplace in the near future.
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                Author and article information

                Contributors
                Bailin Hao
                Journal
                Journal ID (nlm-ta): Genomics Proteomics Bioinformatics
                Journal ID (iso-abbrev): Genomics Proteomics Bioinformatics
                Title: Genomics, Proteomics & Bioinformatics
                Publisher: Elsevier
                ISSN (Print): 1672-0229
                ISSN (Electronic): 2210-3244
                Publication date PMC-release: 05 March 2011
                Publication date (Print): December 2010
                Publication date (Electronic): 05 March 2011
                Volume: 8
                Issue: 4
                Pages: 262-267
                Affiliations
                [1 ]T-Life Research Center & Department of Physics, Fudan University, Shanghai 200433, China
                [2 ]Shanghai Institute of Applied Physics, Chinese Acadamy of Sciences, Shanghai 201800, China
                [3 ]Applied Biosystems, Inc., Beijing 100027, China
                [4 ]Fudan-VARI Center for Genetic Epidemiology, Fudan University, Shanghai 200433, China
                [5 ]Institute of Theoretical Physics, Chinese Acadamy of Sciences, Beijing 100190, China
                [6 ]Santa Fe Institute, Santa Fe, NM 87505, USA
                Author notes
                [* ]Corresponding author. hao@ 123456mail.itp.ac.cn
                Article
                Publisher ID: S1672-0229(10)60028-9
                DOI: 10.1016/S1672-0229(10)60028-9
                PMC ID: 5054193
                PubMed ID: 21382595
                SO-VID: f3162665-ac42-4af2-b933-56b717a89c7c
                Copyright statement: © 2010 Beijing Institute of Genomics
                License:

                This is an open access article under the CC BY-NC-SA license (http://creativecommons.org/licenses/by-nc-sa/3.0/).

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                Categories
                Subject: Method

                Keywords: composition vector,phylogeny,topological distance,bootstrap,jackknife,cvtree
                Data availability:
                Keywords: composition vector, phylogeny, topological distance, bootstrap, jackknife, cvtree

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