PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance.
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.
Deng
Riqiang
R
State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China.
Huang
Mingsong
M
Wang
Jinwen
J
Huang
Yuansen
Y
Yang
Jie
J
Feng
Jinghua
J
Wang
Xunzhang
X
D000465:Algorithms; D000818:Animals; D019295:Computational Biology; D004247:DNA / Q000737:chemistry / Q000235:genetics*; D030541:Databases, Genetic; D016678:Genome; D006801:Humans; D010802:Phylogeny; D011995:Recombination, Genetic / Q000235:genetics; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods
D004247:DNA