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.
Keywords for this software
References in zbMATH (referenced in 1 article )
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- Deng, Riqiang; Huang, Mingsong; Wang, Jinwen; Huang, Yuansen; Yang, Jie; Feng, Jinghua; Wang, Xunzhang: PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance (2006)