title: SNPGenie: estimating evolutionary parameters to detect natural selection using pooled next-generation sequencing data.
abstract: New applications of next-generation sequencing technologies use pools of DNA from multiple individuals to estimate population genetic parameters. However, no publicly available tools exist to analyse single-nucleotide polymorphism (SNP) calling results directly for evolutionary parameters important in detecting natural selection, including nucleotide diversity and gene diversity. We have developed SNPGenie to fill this gap. The user submits a FASTA reference sequence(s), a Gene Transfer Format (.GTF) file with CDS information and a SNP report(s) in an increasing selection of formats. The program estimates nucleotide diversity, distance from the reference and gene diversity. Sites are flagged for multiple overlapping reading frames, and are categorized by polymorphism type: nonsynonymous, synonymous, or ambiguous. The results allow single nucleotide, single codon, sliding window, whole gene and whole genome/population analyses that aid in the detection of positive and purifying natural selection in the source population.
  
  
  METHODS
  SNPGenie version 1.2 is a Perl program with no additional dependencies. It is free, open-source, and available for download at https://github.com/hugheslab/snpgenie.
  
  
  BACKGROUND
  nelsoncw@email.sc.edu or austin@biol.sc.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA and.
authors.forename: Chase W
authors.initials: CW
authors.lastname: Nelson
authors.affiliation: Department of Pathobiological Sciences, University of Wisconsin School of Veterinary Medicine, Madison, WI 53706, USA.
authors.forename: Louise H
authors.initials: LH
authors.lastname: Moncla
authors.affiliation: Department of Biological Sciences, University of South Carolina, Columbia, SC 29208, USA and.
authors.forename: Austin L
authors.initials: AL
authors.lastname: Hughes
mesh_terms: D005075:Biological Evolution; D005828:Genetics, Population; D006388:Hemagglutinins / Q000235:genetics; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D006801:Humans; D053124:Influenza A Virus, H5N1 Subtype / Q000235:genetics; D009439:Neuraminidase / Q000235:genetics; D020641:Polymorphism, Single Nucleotide / Q000235:genetics*; D012641:Selection, Genetic; D012984:Software
chemical_list: D006388:Hemagglutinins; D009439:Neuraminidase