title: micropan: an R-package for microbial pan-genomics.
abstract: BACKGROUND
  A pan-genome is defined as the set of all unique gene families found in one or more strains of a prokaryotic species. Due to the extensive within-species diversity in the microbial world, the pan-genome is often many times larger than a single genome. Studies of pan-genomes have become popular due to the easy access to whole-genome sequence data for prokaryotes. A pan-genome study reveals species diversity and gene families that may be of special interest, e.g because of their role in bacterial survival or their ability to discriminate strains.
  
  
  RESULTS
  We present an R package for the study of prokaryotic pan-genomes. The R computing environment harbors endless possibilities with respect to statistical analyses and graphics. External free software is used for the heavy computations involved, and the R package provides functions for building a computational pipeline.
  
  
  CONCLUSIONS
  We demonstrate parts of the package on a data set for the gram positive bacterium Enterococcus faecalis. The package is free to download and install from The Comprehensive R Archive Network.
authors.affiliation: Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway. lars.snipen@nmbu.no.
authors.forename: Lars
authors.initials: L
authors.lastname: Snipen
authors.affiliation: Department of Chemistry, Biotechnology and Food Sciences, Norwegian University of Life Sciences, P.O. Box 5003, N-1432, Ås, Norway. kristian.liland@nofima.no.|Nofima - Norwegian Institute of Food, Fisheries and Aquaculture Research, Osloveien 1, N-1430, Ås, Norway. kristian.liland@nofima.no.
authors.forename: Kristian Hovde
authors.initials: KH
authors.lastname: Liland
mesh_terms: D000465:Algorithms; D019295:Computational Biology / Q000379:methods*; D016983:Enterococcus / Q000145:classification / Q000235:genetics*; D016680:Genome, Bacterial; D023281:Genomics / Q000379:methods*; D012984:Software