Jackknife and bootstrap tests of the composition vector trees.
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TLDR
The stability and self-consistency of CVTrees are shown by performing bootstrap and jackknife re-sampling tests adapted to this alignment-free approach to estimate prokaryotic phylogenetic trees.About:
This article is published in Genomics, Proteomics & Bioinformatics.The article was published on 2010-12-01 and is currently open access. It has received 26 citations till now. The article focuses on the topics: Jackknife resampling.read more
Citations
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Journal ArticleDOI
CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.
Guanghong Zuo,Bailin Hao +1 more
TL;DR: The power of the new server is described for the mega-classification of prokaryotes and determination of taxonomic placement of some newly-sequenced genomes.
Journal ArticleDOI
Insights on the Evolution of Mycoparasitism from the Genome of Clonostachys rosea
Magnus Karlsson,Mikael Brandström Durling,Jaeyoung Choi,Chatchai Kosawang,Gerald Lackner,Georgios Tzelepis,Kristiina Nygren,Mukesh Dubey,Nathalie N. Kamou,Anthony Levasseur,Antonio Zapparata,Jinhui Wang,Daniel Buchvaldt Amby,Birgit Jensen,Sabrina Sarrocco,Emmanuel Panteris,Anastasia L. Lagopodi,Stefanie Pöggeler,Giovanni Vannacci,David B. Collinge,Dirk Hoffmeister,Bernard Henrissat,Yong-Hwan Lee,Dan Funck Jensen +23 more
TL;DR: The genome sequencing and comparative genome analysis suggest that tolerance toward secondary metabolites is a prominent feature in the biology of C. rosea and that the evolution of mycoparasitism as a fungal lifestyle is being studied.
Journal ArticleDOI
Composition-based classification of short metagenomic sequences elucidates the landscapes of taxonomic and functional enrichment of microorganisms
TL;DR: To the knowledge, MetaCV, benefited from the strategy of composition comparison, is the first algorithm that can classify millions of very short reads within affordable time and has a high resolution to characterize the composition and structure of human gut microbiota.
Journal ArticleDOI
funRNA: a fungi-centered genomics platform for genes encoding key components of RNAi
Jaeyoung Choi,Ki-Tae Kim,Jongbum Jeon,Jiayao Wu,Hyeunjeong Song,Fred O. Asiegbu,Yong-Hwan Lee +6 more
TL;DR: FunRNA is presented, a fungal kingdom-wide comparative genomics platform for putative genes encoding Argonaute, Dicer, and RdRP that could serve as a versatile genomics workbench for key components of RNAi.
Journal ArticleDOI
Shigella Strains Are Not Clones of Escherichia coli but Sister Species in the Genus Escherichia
Guanghong Zuo,Zhao Xu,Bailin Hao +2 more
TL;DR: The whole-genome-based, alignment-free and parameter-free CVTree approach shows convincingly that four established Shigella species are distinct from E. coli strains, and form sister species to E. bacteria within the genus Escherichia.
References
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Journal ArticleDOI
The neighbor-joining method: a new method for reconstructing phylogenetic trees.
Naruya Saitou,Masatoshi Nei +1 more
TL;DR: The neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods for reconstructing phylogenetic trees from evolutionary distance data.
Book
Molecular Evolution and Phylogenetics
Masatoshi Nei,Sudhir Kumar +1 more
TL;DR: This chapter discusses the molecular basis of evolution, the evolution of organisms based on the fossil record, and the implications of these events for phylogenetic inference.
Journal ArticleDOI
Comparison of phylogenetic trees
D. F. Robinson,L. R. Foulds +1 more
TL;DR: The metric presented in this paper makes possible the comparison of the many nonbinary phylogenetic trees appearing in the literature, and provides an objective procedure for comparing the different methods for constructing phylogenetics trees.
Journal ArticleDOI
A Simple Method for Estimating and Testing Minimum-Evolution Trees
Andrey Rzhetsky,Masatoshi Nei +1 more
TL;DR: Both a mathematical method for computing the number of trees with a given value of topological difference from the NJ tree and a computer algorithm for identifying all the topologies are developed.
Journal ArticleDOI
Whole proteome prokaryote phylogeny without sequence alignment: a K-string composition approach.
Ji Qi,Bin Wang,Bai-Iin Hao +2 more
TL;DR: 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 and 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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