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CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes
Xu, Zhao; Hao, Bailin; Xu, Z , Fudan Univ, T Life Res Ctr, 220 Handan Rd, Shanghai 200433, Peoples R China
2009
发表期刊NUCLEIC ACIDS RESEARCH
ISSN0305-1048
卷号37期号:suppl.2页码:W174-W178
摘要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.
部门归属[Xu, Z; Hao, BL] Fudan Univ, T Life Res Ctr, Shanghai 200433, Peoples R China; [Hao, BL] Acad Sinica, Inst Theoret Phys, Beijing 100190, Peoples R China; [Hao, BL] Santa Fe Inst, Santa Fe, NM 87501 USA
关键词Prokaryote Phylogeny Molecular Phylogeny Trees Reconstruction Life Tool
学科领域Physics
资助者National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111]
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资助者National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111] ; National Basic Research Program of China[2007CB814800]; Shanghai Leading Academic Discipline Project[B111]
WOS记录号WOS:000267889100032
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被引频次:104[WOS]   [WOS记录]     [WOS相关记录]
文献类型期刊论文
条目标识符http://ir.itp.ac.cn/handle/311006/5287
专题理论物理所1978-2010年知识产出
通讯作者Xu, Z , Fudan Univ, T Life Res Ctr, 220 Handan Rd, Shanghai 200433, Peoples R China
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Xu, Zhao,Hao, Bailin,Xu, Z , Fudan Univ, T Life Res Ctr, 220 Handan Rd, Shanghai 200433, Peoples R China. CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes[J]. NUCLEIC ACIDS RESEARCH,2009,37(suppl.2):W174-W178.
APA Xu, Zhao,Hao, Bailin,&Xu, Z , Fudan Univ, T Life Res Ctr, 220 Handan Rd, Shanghai 200433, Peoples R China.(2009).CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes.NUCLEIC ACIDS RESEARCH,37(suppl.2),W174-W178.
MLA Xu, Zhao,et al."CVTree update: a newly designed phylogenetic study platform using composition vectors and whole genomes".NUCLEIC ACIDS RESEARCH 37.suppl.2(2009):W174-W178.
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