title: Strainer: software for analysis of population variation in community genomic datasets.
abstract: BACKGROUND
  Metagenomic analyses of microbial communities that are comprehensive enough to provide multiple samples of most loci in the genomes of the dominant organism types will also reveal patterns of genetic variation within natural populations. New bioinformatic tools will enable visualization and comprehensive analysis of this sequence variation and inference of recent evolutionary and ecological processes.
  
  
  RESULTS
  We have developed a software package for analysis and visualization of genetic variation in populations and reconstruction of strain variants from otherwise co-assembled sequences. Sequencing reads can be clustered by matching patterns of single nucleotide polymorphisms to generate predicted gene and protein variant sequences, identify conserved intergenic regulatory sequences, and determine the quantity and distribution of recombination events.
  
  
  CONCLUSIONS
  The Strainer software, a first generation metagenomic bioinformatics tool, facilitates comprehension and analysis of heterogeneity intrinsic in natural communities. The program reveals the degree of clustering among closely related sequence variants and provides a rapid means to generate gene and protein sequences for functional, ecological, and evolutionary analyses.
authors.affiliation: Department of Environmental Science, Policy and Management, University of California, Berkeley, CA 94720, USA. jmeppley@gmail.com
authors.forename: John M
authors.initials: JM
authors.lastname: Eppley
authors.forename: Gene W
authors.initials: GW
authors.lastname: Tyson
authors.forename: Wayne M
authors.initials: WM
authors.lastname: Getz
authors.forename: Jillian F
authors.initials: JF
authors.lastname: Banfield
mesh_terms: D001483:Base Sequence; D002874:Chromosome Mapping / Q000379:methods*; D004252:DNA Mutational Analysis / Q000379:methods*; D030541:Databases, Genetic; D014644:Genetic Variation / Q000235:genetics*; D005828:Genetics, Population / Q000379:methods; D016680:Genome, Bacterial / Q000235:genetics*; D008969:Molecular Sequence Data; D016415:Sequence Alignment / Q000379:methods; D017422:Sequence Analysis, DNA / Q000379:methods*; D012984:Software; D013045:Species Specificity