PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance

被引：10

作者：

Deng, Riqiang ^{[1
]}

Huang, Mingsong ^{[1
]}

Wang, Jinwen ^{[1
]}

Huang, Yuansen ^{[1
]}

Yang, Jie ^{[1
]}

Feng, Jinghua ^{[1
]}

Wang, Xunzhang ^{[1
]}

机构：

[1] Zhongshan Univ, Sch Life Sci, State Key Lab Biocontrol, Guangzhou 510275, Peoples R China

来源：

COMPUTATIONAL BIOLOGY AND CHEMISTRY | 2006年 / 30卷 / 04期

基金：

中国国家自然科学基金;

关键词：

phylogenetic tree; whole-genome sequences; PTreeRec; maximal segment pairs; BLAST distance;

D O I：

10.1016/j.compbiolchem.2006.04.003

中图分类号：

Q [生物科学];

学科分类号：

07 ; 0710 ; 09 ;

摘要：

Phylogenetic Tree Reconstruction (PTreeRec) is a web-based tool for automatic phylogeny inferences from whole-genome sequences, which accepts files of DNA sequences in the FASTA format and allows users to save the output tree file, and displays the inferred tree through an applet in a web browser. PTreeRec involves three basic steps. First, regions of maximal segment pairs (MSPs) based on an all-against-all pairwise comparison of genomes are located. Second, a distance matrix is calculated from MSP scores or coverage. Finally, a phylogenetic tree is reconstructed by the neighbor-joining method. (c) 2006 Elsevier Ltd. All rights reserved.

引用

页码：300 / 302

页数：3

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