Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes

Faison, William J.; Rostovtsev, Alexandre; Castro-Nallar, Eduardo; Crandall, Keith A.; Chumakov, Konstantin; Simonyan, Vahan; Mazumder, Raja


Next-generation sequencing data can be mapped to a reference genome to identify single-nucleotide polymorphisms/variations (SNPs/SNVs; called SNPs hereafter). In theory, SNPs can be compared across several samples and the differences can be used to create phylogenetic trees depicting relatedness among the samples. However, in practice this is difficult because currently there is no stand-alone tool that takes SNP data directly as input and produces phylogenetic trees. In response to this need, PhyloSNP application was created with two analysis methods 1) a quantitative method that creates the presence/absence matrix which can be directly used to generate phylogenetic trees or creates a tree from a shrunk genome alignment (includes additional bases surrounding the SNP position) and 2) a qualitative method that clusters samples based on the frequency of different bases found at a particular position. The algorithms were used to generate trees from Poliovirus, Burkholderia and human cancer genomics NGS datasets. (C) 2014 Elsevier Inc. All rights reserved.

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Título según WOS: ID WOS:000340021500001 Not found in local WOS DB
Título de la Revista: GENOMICS
Volumen: 104
Número: 1
Fecha de publicación: 2014
Página de inicio: 1
Página final: 7


Notas: ISI