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PTreeRec: Phylogenetic Tree Reconstruction based on genome BLAST distance. (English) Zbl 1099.92054

Summary: 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.

MSC:

92D15 Problems related to evolution

Software:

ATV; PTreeRec; PHYLIP
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Full Text: DOI

References:

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