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

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

Research output: Contribution to journalArticlepeer-review

12 Citations (Scopus)

Abstract

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.Availability: PhyloSNP is freely available for download at http://hive.biochemistry.gwu.edu/dna.cgi?cmd=phylosnp.

Original languageEnglish
Pages (from-to)1-7
Number of pages7
JournalGenomics
Volume104
Issue number1
DOIs
Publication statusPublished - Jul 2014

Keywords

  • Cancer genomics
  • Next-generation sequencing
  • Phylogenetic
  • SNP
  • SNV
  • Vaccine quality control

ASJC Scopus subject areas

  • Genetics

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