title: Whole genome single-nucleotide variation profile-based phylogenetic tree building methods for analysis of viral, bacterial and human genomes.
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.
  
  
  BACKGROUND
  PhyloSNP is freely available for download at http://hive.biochemistry.gwu.edu/dna.cgi?cmd=phylosnp.
authors.affiliation: The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA. Electronic address: Jamie_Faison@gwmail.gwu.edu.
authors.forename: William J
authors.initials: WJ
authors.lastname: Faison
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, 1451 Rockville Pike, Rockville, MD 20852, USA. Electronic address: Alexandre.Rostovtsev@fda.hhs.gov.
authors.forename: Alexandre
authors.initials: A
authors.lastname: Rostovtsev
authors.affiliation: Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA. Electronic address: Ecastron@gwmail.gwu.edu.
authors.forename: Eduardo
authors.initials: E
authors.lastname: Castro-Nallar
authors.affiliation: Computational Biology Institute, George Washington University, Ashburn, VA 20147, USA. Electronic address: Kcrandall@gwu.edu.
authors.forename: Keith A
authors.initials: KA
authors.lastname: Crandall
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, 1451 Rockville Pike, Rockville, MD 20852, USA. Electronic address: Konstantin.Chumakov@fda.hhs.gov.
authors.forename: Konstantin
authors.initials: K
authors.lastname: Chumakov
authors.affiliation: Center for Biologics Evaluation and Research, US Food and Drug Administration, 1451 Rockville Pike, Rockville, MD 20852, USA. Electronic address: Vahan.Simonyan@fda.hhs.gov.
authors.forename: Vahan
authors.initials: V
authors.lastname: Simonyan
authors.affiliation: The Department of Biochemistry & Molecular Medicine, George Washington University Medical Center, Washington, DC 20037, USA; McCormick Genomic and Proteomic Center, George Washington University, Washington, DC 20037, USA. Electronic address: Mazumder@gwu.edu.
authors.forename: Raja
authors.initials: R
authors.lastname: Mazumder
mesh_terms: D000465:Algorithms; D016957:Burkholderia pseudomallei / Q000235:genetics*; D015894:Genome, Human; D023281:Genomics / Q000379:methods*; D006801:Humans; D010802:Phylogeny; D017955:Poliovirus / Q000235:genetics*; D020641:Polymorphism, Single Nucleotide; D016415:Sequence Alignment / Q000379:methods*; D012984:Software
keywords: Cancer genomics; Next-generation sequencing; Phylogenetic; SNP; SNV; Vaccine quality control