title: PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance.
abstract: 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.
authors.affiliation: State Key Laboratory of Biocontrol, School of Life Science, Sun Yat-sen (Zhongshan) University, Guangzhou 510275, People's Republic of China.
authors.forename: Riqiang
authors.initials: R
authors.lastname: Deng
authors.forename: Mingsong
authors.initials: M
authors.lastname: Huang
authors.forename: Jinwen
authors.initials: J
authors.lastname: Wang
authors.forename: Yuansen
authors.initials: Y
authors.lastname: Huang
authors.forename: Jie
authors.initials: J
authors.lastname: Yang
authors.forename: Jinghua
authors.initials: J
authors.lastname: Feng
authors.forename: Xunzhang
authors.initials: X
authors.lastname: Wang
mesh_terms: 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
chemical_list: D004247:DNA