Literature DB >> 20036699

Composition vector approach to whole-genome-based prokaryotic phylogeny: success and foundations.

Qiang Li1, Zhao Xu, Bailin Hao.   

Abstract

Composition vector approach to prokaryotic phylogeny provides an alignment-free and parameter-free method based on whole-genome data. It has also been applied to viruses and fungi. In all studied cases the inferred phylogenetic relationships agree well with taxonomic knowledge in major groupings and fine branchings. In this review article, after demonstrating its successful application to a collection of 892 genomes including 62 Archaea, 822 Bacteria and 8 Eukarya, we will outline some ongoing work towards the foundations of this new approach. Copyright 2009 Elsevier B.V. All rights reserved.

Mesh：

Year:  2009        PMID： 20036699     DOI： 10.1016/j.jbiotec.2009.12.015

Source DB:  PubMed          Journal:  J Biotechnol        ISSN： 0168-1656            Impact factor:   3.307


  18 in total

Review 1.  New developments of alignment-free sequence comparison: measures, statistics and next-generation sequencing.

Authors:  Kai Song; Jie Ren; Gesine Reinert; Minghua Deng; Michael S Waterman; Fengzhu Sun
Journal:  Brief Bioinform       Date:  2013-09-23       Impact factor: 11.622

2.  Cyanobacterial phylogenetic analysis based on phylogenomics approaches render evolutionary diversification and adaptation: an overview of representative orders.

Authors:  Ratna Prabha; Dhananjaya P Singh
Journal:  3 Biotech       Date:  2019-02-15       Impact factor: 2.406

3.  Phylogenomics of the Phylum Proteobacteria: Resolving the Complex Relationships.

Authors:  Vaibhav Sharma; Amit Vashishtha; Arsha Liz M Jos; Akshita Khosla; Nirmegh Basu; Rishabh Yadav; Amit Bhatt; Akshanshi Gulani; Pushpa Singh; Sanidhya Lakhera; Mansi Verma
Journal:  Curr Microbiol       Date:  2022-06-15       Impact factor: 2.188

4.  CGAP: a new comprehensive platform for the comparative analysis of chloroplast genomes.

Authors:  Jinkui Cheng; Xu Zeng; Guomin Ren; Zhihua Liu
Journal:  BMC Bioinformatics       Date:  2013-03-14       Impact factor: 3.169

5.  Prokaryotic phylogenies inferred from whole-genome sequence and annotation data.

Authors:  Wei Du; Zhongbo Cao; Yan Wang; Ying Sun; Enrico Blanzieri; Yanchun Liang
Journal:  Biomed Res Int       Date:  2013-08-29       Impact factor: 3.411

6.  Geographic divergence of "Sulfolobus islandicus" strains assessed by genomic analyses including electronic DNA hybridization confirms they are geovars.

Authors:  Guanghong Zuo; Bailin Hao; James T Staley
Journal:  Antonie Van Leeuwenhoek       Date:  2013-12-04       Impact factor: 2.271

7.  Genome sequence reveals that Pseudomonas fluorescens F113 possesses a large and diverse array of systems for rhizosphere function and host interaction.

Authors:  Miguel Redondo-Nieto; Matthieu Barret; John Morrissey; Kieran Germaine; Francisco Martínez-Granero; Emma Barahona; Ana Navazo; María Sánchez-Contreras; Jennifer A Moynihan; Candela Muriel; David Dowling; Fergal O'Gara; Marta Martín; Rafael Rivilla
Journal:  BMC Genomics       Date:  2013-01-25       Impact factor: 3.969

8.  CVTree3 Web Server for Whole-genome-based and Alignment-free Prokaryotic Phylogeny and Taxonomy.

Authors:  Guanghong Zuo; Bailin Hao
Journal:  Genomics Proteomics Bioinformatics       Date:  2015-11-10       Impact factor: 7.691

9.  Alignment-free genome tree inference by learning group-specific distance metrics.

Authors:  Kaustubh R Patil; Alice C McHardy
Journal:  Genome Biol Evol       Date:  2013       Impact factor: 3.416

10.  Phylogenetic and biological significance of evolutionary elements from metazoan mitochondrial genomes.

Authors:  Jianbo Yuan; Qingming Zhu; Bin Liu
Journal:  PLoS One       Date:  2014-01-20       Impact factor: 3.240
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